Method for preparing biological material having excellent light-transmitting property

ABSTRACT

The present invention relates to a clearing technique which uses a solution containing at least one of a compound having a delipidation ability, a compound having a biochrome decoloring ability, a compound having a decalcification ability, a compound having a refractive index adjusting ability, and a compound having a tissue swelling ability. The clearing technique is suitable for use in high-throughput and low-magnification imaging which involves a simple process.

TECHNICAL FIELD

The present invention relates to a composition for preparing a biological material having an excellent light-transmitting property and to use of the composition.

BACKGROUND ART

For high-level observations of gene expression within tissue, intracellular localization, and cell morphology, a pretreatment (clearing treatment) for increasing the light-transmitting property of tissue has been performed with use of a clearing reagent in recent years. Various clearing reagents and pretreatment methods have thus been developed.

For example, Non Patent Literatures 1 and 2 each disclose a clearing treatment technique involving use of benzylbenzoate/benzylalcohol (BABB method). The BABB method is a classic tissue clearing method involving use of an organic solvent, and has been applied as a method for preparing a cleared sample to be observed through a light-sheet macro-zoom microscope.

Non Patent Literature 3 discloses a technique (SeeDB method) of adjusting the refractive index with use of fructose. The SeeDB method is primarily intended to minimize a change caused to biological tissue during the treatment, and thus the biological tissue substantially completely maintains the molecular-level structure, membrane structure, axon shape, and the like. The SeeDB method, in a case where it uses a two-photon microscope and an optimized lens, allows observation at a level of the whole brain.

Non Patent Literature 4 and Patent Literature 1 each disclose a technique (Scale method) that uses a water-soluble reagent to successfully minimize quenching of fluorescence signals. This technique is also primarily intended to minimize a change caused to biological tissue during the treatment, and is mainly intended for use in axon observation in neuroscience, detection of an amyloid plaque in tissue affected by Alzheimer's disease, and the like.

Non Patent Literature 5 discloses a clearing technique (CLARITY method) based on a physicochemical method involving use of an electrophoresis apparatus. The CLARITY method uses an electrophoresis apparatus to physicochemically treat brain tissue packed with use of an acrylamide polymer for removal of lipid components to make the brain tissue transparent. The CLARITY method allows high-level clearing in approximately two weeks in a state where the molecular-level structure of tissue is maintained. The CLARITY method is applicable to both (i) fluorescent protein labeling and (ii) immunostaining.

Non-patent Literature 6 discloses clearing techniques (PACT method, PARS method) which, as a way of improvement from the difficult physicochemical method involving use of an electrophoresis apparatus in the CLARITY method, involve perfusion with use of an SDS (detergent) solution which is used in the CLARITY method.

Non-patent Literature 7 discloses a clearing technique (SWITCH method) which, as a way of improvement from the difficult physicochemical method involving use of an electrophoresis apparatus in the CLARITY method, involves high-temperature treatment of an SDS (detergent) solution which is used in the CLARITY method.

CITATION LIST Patent Literature

-   [Patent Literature 1] -   International Publication No. WO2012/161143

Non-Patent Literatures

-   [Non-patent Literature 1] -   Hans-Ulrich Dodt et al., “Ultramicroscopy: three-dimensional     visualization of neuronal networks in the whole mouse brain”, Nature     Methods, vol. 4, No. 4: 331-336 (2007) -   [Non-patent Literature 2] -   Klaus Becker et al., “Chemical Clearing and Dehydration of GFP     Expressing Mouse Brains”, PLoS ONE, vol. 7, issue 3: e33916 (2012) -   [Non-patent Literature 3] -   Meng-Tsen Ke et al., “SeeDB: a simple and morphology-preserving     optical clearing agent for neuronal circuit reconstruction”, advance     online publication (published online 23 Jun. 2013) -   [Non-patent Literature 4] -   Hiroshi Hama et al., “Scale: a chemical approach for fluorescence     imaging and reconstruction of transparent mouse brain”, Nature     Neuroscience, vol. 14, No. 11: 1481-1490 (2011) -   [Non-patent Literature 5] -   Kwanghun Chung et al., “Structural and molecular interrogation of     intact biological systems”, Nature, vol. 497: 332-339 (2013) -   [Non-patent Literature 6] -   Bin Yang et al., “Single-Cell Phenotyping within Transparent Intact     Tissue through Whole-Body Clearing”, Cell, vol. 158: 945-958 (2014) -   [Non-patent Literature 7] -   Evan Murray et al., “Simple, Scalable Proteomic Imaging for     High-Dimensional Profiling of Intact Systems”, Cell, vol. 163:     1500-1514 (2015)

SUMMARY OF INVENTION Technical Problem

However, according to the BABB method described in each of Non Patent Literatures 1 and 2, disappearance of a fluorescent protein occurs significantly due to a dehydration process and an organic solvent treatment, and signal detection thus becomes impossible within a short time. In addition, organic solvents in general have a safety concern.

The SeeDB method, described in Non Patent Literature 3, allows observation at a whole-brain level, but requires several days for scanning. Further, the SeeDB method is assumed to be applied to a two-photon microscope, and the transparency of tissue treated (adult brain in particular) is thus not high enough for observation through a microscope of a light-sheet system.

The Scale method described in Non-patent Literature 4 is assumed to be applied to a confocal microscope and a two-photon microscope, and the transparency of tissue treated (adult brain in particular) is thus not high enough for observation through a microscope of a light-sheet system.

The CLARITY method, described in Non Patent Literature 5, and the PACT method and the PARS method, described in Non-patent Literature 6, each involve a complicated process and require a dedicated device. The CLARITY method, the PACT method, and the PARS method are thus not suited for multiple samples.

The SWITCH method described in Non-patent Literature requires a high-temperature treatment with use of a detergent, and disappearance of a fluorescent protein is thus significant.

The present invention has been accomplished to solve the above problems. It is an object of the present invention to provide a clearing technique which uses a simple process and is suitable for use in high-throughput and low-magnification imaging.

Solution to Problem

In order to solve the above problems, the inventors of the present invention conducted a large-scale screening on the basis of various unique viewpoints. As a result, the inventors of the present invention found a plurality of compounds which are capable of making a biological material transparent. Thus, the inventors of the present invention completed the present invention.

That is, a composition in accordance with the present invention is a composition for preparing a biological material having an excellent light-transmitting property, the composition being a solution containing at least one of: (A) a compound having a high delipidation ability; (B) a compound exhibiting a decoloring activity higher than that of N,N,N′,N′-tetrakis(2-hydroxypropyl)ethylenediamine; (C) a combination of EDTA, an acid, and a base; (D) a compound which is soluble at a concentration of 60 wt % or more in water and which allows an aqueous solution, in which the compound (D) is contained at a concentration that is at least one value within a range of 60 wt % to 80 wt %, to have a refractive index of 1.47 to 1.50; and (E) a compound exhibiting a swelling activity higher than that of urea.

A method in accordance with the present invention is a method for preparing a biological material having an excellent light-transmitting property, the method comprising the step of: permeating into a biological material a solution containing at least one of the above-described (A) to (E).

A biological material having an excellent light-transmitting property in accordance with the present invention is a biological material which has been permeated with a solution containing at least one of the above-described (A) to (E).

Advantageous Effects of Invention

The present invention is a technique based on a chemical treatment, and does not require employment of specialized equipment and a complicated manipulation. Further, the present invention uses a simple process to make it possible to make a biological material transparent at a level high enough for a high-throughput analysis of multiple samples.

BRIEF DESCRIPTION OF DRAWINGS

FIG. 1 is a view showing a correlation between delipidation activity and compound category in an Example of the present invention.

FIG. 2 is a view showing a correlation between delipidation activity and pH in an Example of the present invention.

FIG. 3 is a view showing clearing of mouse hemispheres and efficiency of delipidation of the mouse hemispheres in an Example of the present invention.

FIG. 4 is a view showing a correlation between transparency and phospholipid content of a mouse hemisphere in an Example of the present invention.

FIG. 5 is a view showing a comparison of clearing of human brain white matter with use of 10 wt % #0070+each 10 wt % chemical in an Example of the present invention.

FIG. 6 is a view showing a comparison of clearing of human brain white matter caused with use of 10 wt % #0070+each 10 wt % detergent in an Example of the present invention.

FIG. 7 is a view showing a correlation between fluorescence intensity of EGFP and pH in an Example of the present invention.

FIG. 8 is a view showing a comparison of transparency of a mouse hemisphere in a case of using each basic chemical in an Example of the present invention.

FIG. 9 is a view showing clearing of a mouse kidney and efficiency of delipidation of the mouse kidney in a case of using 10 wt % #0414+each 10 wt % chemical in an Example of the present invention.

FIG. 10 is a view showing efficiency of quenching of EGFP in a case of using each #0414 cocktail in an Example of the present invention.

FIG. 11 is a view showing clearing of a mouse whole brain with use of 10 wt % #0414+10 wt % Triton X-100 in an Example of the present invention.

FIG. 12 is a view showing efficiency of decoloring of a mouse spleen in an Example of the present invention.

FIG. 13 is a view showing clearing of a mouse femur and fluorescence quenching of GFP in a case of using each EDTA cocktail in an Example of the present invention.

FIG. 14 is a view showing a solubility test of a hydroxyapatite suspension in an Example of the present invention.

FIG. 15 is a view showing pH-dependency of solubilization of a hydroxyapatite suspension with use of each EDTA+#0414 cocktail in an Example of the present invention.

FIG. 16 is a view showing temperature-dependency and EDTA concentration-dependency of solubilization of a hydroxyapatite suspension with use of each EDTA+#0414 cocktail in an Example of the present invention.

FIG. 17 is a view showing a comparison of decalcification activity in a case of using 10 wt % EDTA+each basic chemical in an Example of the present invention.

FIG. 18 is a view showing clearing of a mouse kidney in a case of using each kind of refractive index adjusting agent in an Example of the present invention.

FIG. 19 is a view showing clearing of a mouse lung caused in a case of using each kind of refractive index adjusting agent in an Example of the present invention.

FIG. 20 is a view showing top compounds in swelling screening performed with use of gelatin in an Example of the present invention.

FIG. 21 is a view showing swelling of a brain which has been subjected to delipidation with use of a reagent #1352 having a swelling activity in an Example of the present invention.

FIG. 22 is a view showing a swollen brain which has been made transparent with use of a #0640+#1352 mixed solution in an Example of the present invention.

FIG. 23 is a view showing clearing of tissue including human brain white matter and a mouse liver in an Example of the present invention.

FIG. 24 is a view showing clearing of mouse brain tissue in an Example of the present invention.

FIG. 25 is a view showing a refractive index adjustment on delipidated tissue in an Example of the present invention.

FIG. 26 is a view showing clearing of mouse organs and a mouse whole body in an Example of the present invention.

FIG. 27 is a view showing clearing of human tissue in an Example of the present invention.

FIG. 28 is a view showing clearing of human brain tissue in an Example of the present invention.

FIG. 29 is a view showing clearing of a marmoset brain in an Example of the present invention.

DESCRIPTION OF EMBODIMENTS

The following description will discuss an embodiment of the present invention in detail.

[1. Composition]

The present invention provides a composition for preparing a biological material having an excellent light-transmitting property. A composition in accordance with the present invention is characterized by being a solution containing at least one (one, two, three, four, or five) of (A) to (E), each of which will be described later.

The term “light-transmitting property” as used in the present invention refers to (i) the proportion of transmitted light with respect to incident light or (ii) what proportion of fluorescence generated by excitation light irradiation passes through and how low scattering of the fluorescence light is. The expression “having an excellent light-transmitting property” means, as an example, that the proportion of outgoing light from an observation target (that is, transmitted light) is large with respect to light incident on the observation target. The light-transmitting property can be expressed as, for example, a percentage such that regarding the proportion of transmitted light with respect to incident light, (i) a substance that blocks light (for example, a black and thick plastic, a metal, or the like) has 0% and (ii) a transparent liquid such as water has 100%. For a biological material in accordance with one embodiment having an excellent light-transmitting property, the proportion of transmitted light with respect to incident light is 40% or more, preferably 50% or more, 60% or more, 70% or more, 80% or more, 90% or more, 95% or more, 98% or more, or 99% or more in terms of light transmittance as measured with use of a spectrophotometer.

A biological material to which the present invention is to be applied is not limited to any particular kind. Preferably, the biological material is a material derived from a plant or an animal, more preferably a material derived from an animal such as one selected from fish, amphibians, reptiles, birds, and mammals, particularly preferably a material derived from a mammal. The mammal is not limited to any particular kind and includes: laboratory animals such as mice, rats, rabbits, guinea pigs, and primates except for humans (such as marmosets); pet animals such as dogs and cats; farm animals such as cows and horses; and humans.

Alternatively, the biological material may be an individual itself (except for a living human individual). Further alternatively, the biological material may be an organ, a tissue, a body fluid (for example, blood, saliva, blood serum, blood plasma, urine, synovial fluid, or spinal fluid), or a cell taken from an individual of a multicellular organism. The organism may be an adult or a fetus. The composition in accordance with the present invention has excellent ability to make a subject transparent; therefore, even if the biological material is a tissue or organ (for example, the whole of or part of the bones, brain, heart, lungs, liver, spleen, or kidneys) derived from a multicellular animal or an individual itself (for example, an embryo or an adult) of a multicellular animal which is not a human, the biological material can be subjected to a clearing treatment. Further, the biological material may be either of (i) a material fixed with use of paraformaldehyde or the like and (ii) a non-fixed material.

Specific examples of the biological material may be: a biological tissue having a fluorescent chemical substance injected therein; a biological tissue stained with a fluorescent chemical substance; a biological tissue having a fluorescent protein-expressed cell transplanted therein; and a biological tissue taken from a genetically-modified animal in which a fluorescent protein is expressed.

The present invention can significantly improve the light-transmitting property of a biological material, and thus allows high-throughput imaging. Specifically, the present invention:

-   -   minimizes quenching of signals of a fluorescent protein or         fluorescent substance;     -   allows multiple samples (several tens to several hundreds of         samples) to be treated simultaneously in parallel;     -   makes a subject so highly transparent that the subject can be         observed under a light-sheet microscope in combination;     -   minimizes the influence on the structuring of a tissue region;         and     -   effectively allows even a large sample (e.g., an adult) made up         of various types of tissue to be made transparent.

Further, a clearing treatment that uses the composition in accordance with the present invention is reversible to a certain extent. Specifically, simply immersing, in an equilibrated salt solution, a biological material that has been subjected to the clearing treatment releases the biological material from a clearing state, so that the non-transparent biological material can be preserved or used in, for example, an immunohistochemical assay or biochemical assay. Specific examples of the balanced salt solution include a balanced salt solution (for example, a PBS or HBSS) buffered with a phosphate; a balanced salt solution (TBS) buffered with tris hydrochloride; a population cerebrospinal fluid (ACSF); and a cell-culture basal medium such as MEM, DMEM, and Ham's F-12. The antigenicity of a protein or the like remains unchanged (preserved) before and after the clearing treatment. This makes it possible to perform analyses with use of a normal tissue-staining technique or immunostaining technique.

((A) Compound Having Delipidation Removal Ability)

A compound (A) which may be contained in the composition in accordance with the present invention is a compound having a delipidation ability. In an example, the compound (A) has a high delipidation ability.

In one embodiment, the compound (A) is such a compound that a mixed solution containing the compound has an OD600 of not more than 0.336 as measured by a method described in the Examples. In another embodiment, the compound (A) is at least one of, for example, a polyether, an anionic detergent, a cationic detergent, an amphoteric detergent, an amine, an aminoalcohol, a polyhydric alcohol, a detergent-like aromatic ether, and a pyridine. From the viewpoint of permeability of the compound (A) with respect to tissue, an amine and a polyalcohol are preferable, and an amine is more preferable.

The amine may be any one of primary amine, secondary amine, tertiary amine, and quaternary amine. The number of amine groups contained in the compound may be one, two, three, four, or more. The amine may have a linear, branched, or cyclic hydrocarbon moiety. The amine may have a saturated or unsaturated hydrocarbon moiety. The amine may have an aromatic ring such as a benzene ring. The number of carbon atoms constituting a hydrocarbon moiety of the amine is not particularly limited, and may be, for example, 1 to 20, 1 to 15, 1 to 10, or 2 to 8.

More specific examples of the compound (A) include compounds shown in Table. 1 and analogs thereof. In one example, #0070 (1,3-bis(aminomethyl)cyclohexane) in Table 1 and an analog thereof are preferable. Examples of the analog of #0070 include bis(aminoalkyl)cycloalkyl. The number of carbon atoms constituting an alkyl in an aminoalkyl group is not particularly limited, and, for example, the number may be 1 to 8, and is 1 in a preferable example. The number of carbon atoms constituting an alkyl in a cycloalkyl moiety is not particularly limited, and, for example, the number may be 3 to 8, and is 6 in a preferable example. The two aminoalkyl groups may be bonded at any position, for example, at “1,2-”, “1,3-”, or “1,4-”. Among the compounds shown in Table. 1 and the analogs thereof, #0070 (1,3-bis(aminomethyl)cyclohexane) in Table. 1 is preferable from the viewpoint of inexpensiveness and less odor.

Further, the compound (A) may be of a single kind or of two or more kinds. In one embodiment, the compound (A) may be a combination of two or more kinds of a polyether, an anionic detergent, a cationic detergent, an amphoteric detergent, an amine, an aminoalcohol, a polyhydric alcohol, a detergent-like aromatic ether, and a pyridine. In one example, it may be preferable to combine an amine and a detergent. Examples of a preferable combination of an amine and a detergent include a combination of #0070 and #0631 and a combination of #0070 and SDS. In particular, the combination of #0070 and #0631 is more preferable.

In a case where the biological material contains a fluorescent protein, it is preferable to use a compound having a pH of 5 to 12, preferably 7 to 11. In particular, from the viewpoint of transparency, #0389 and #0414 are preferable, and #0414 is more preferable. #0414 may be used in combination with another compound. Examples of a preferable combination include a combination of #0414 and Triton X-100, a combination of #0414 and Tween-40, a combination of #0414 and #1051, a combination of #0414 and #0694, and a combination of #0414 and sucrose. In particular, the combination of #0414 and Triton X-100 is more preferable.

The concentration of the compound (A) in the composition is not particularly limited, and, for example, the concentration (in a case where the composition contains two or more compounds, the total concentration of these compounds) is preferably 5 wt % to 60 wt %, more preferably 10 wt % to 40 wt %, further more preferably 15 wt % to 30 wt %. In one example, in a case where an amine and a detergent are combined, the concentration of the amine may be 10 wt % to 20 wt % and the concentration of the detergent may be 5 wt % to 10 wt %.

((B) Compound Having Biochrome Decoloring Ability)

A compound (B) which may be contained in the composition in accordance with the present invention is a compound having a biochrome decoloring ability. In one example, the compound (B) has a high biochrome decoloring ability.

In one embodiment, the compound (B) is a compound exhibiting a decoloring activity higher than that of an aminoalcohol (N,N,N′,N′-tetrakis(2-hydroxypropyl)ethylenediamine). The decoloring activity can be measured, for example, by a method described in the Examples.

In another embodiment, the compound (B) is at least one of, for example, phosphine, alkyl imidazole, a detergent, an amine, a pyridine, an aminoalcohol, an alcohol, benzylamide, and pyrazolone.

More specific examples of the compound (B) include compounds shown in Table. 2 and analogs thereof. In one example, the compound (B) is preferably one which allows fluorescence of a fluorescent protein to be retained, and examples of such a compound include #0441, #0470, #0484, #0635, #0651, #0938, and #1283 shown in Table. 2 and analogs thereof.

From the viewpoint of allowing retention of fluorescence of a fluorescent protein and exhibiting a high decoloring activity, #0651, #0938, and analogs thereof are preferable, and #0938 and an analog thereof are more preferable.

Examples of the analog of #0938 include a compound encompassed in alkyl imidazoles. The alkyl group may be linear, branched, or cyclic. The alkyl group may be saturated or unsaturated. The number of carbon atoms constituting the alkyl group is not particularly limited, and may be, for example, 1 to 20, 1 to 15, 1 to 10, 1 to 8, 1 to 6, 1 to 5, 1 to 4, 1 to 3, or 1 to 2. The position at which the alkyl group is bonded is not particularly limited, but is preferably the first position (1-alkyl imidazole). From the viewpoint of inexpensiveness, 1-methylimidazole is preferable.

The compound (B) may be of a single kind or of two or more kinds.

The concentration of the compound (B) in the composition is not particularly limited, and, for example, the concentration (in a case where the composition contains two or more compounds, the total concentration of these compounds) is preferably 5 wt % to 40 wt %, more preferably 5 wt % to 30 wt %, and further more preferably 10 wt % to 20 wt %.

In one example, the compound (B) has high affinity for heme, and allows detaching heme from hemoglobin without destroying a protein.

((C) Compound Having Decalcification Ability)

A compound (C) which may be contained in the composition in accordance with the present invention is a compound having a decalcification ability. In one example, the compound (C) has a high decalcification ability.

In one embodiment, the compound (C) is a combination of EDTA (ethylenediaminetetraacetic acid), an acid, and a base. Combining the EDTA, the acid, and the base enables efficient decalcification. In one example, quenching of signals of a fluorescent protein is minimized.

Examples of the acid include halogenated monocarboxylic acid, hydroxymonocarboxylic acid, aliphatic monocarboxylic acid, alkyl amino monocarboxylic acid, acetylamino monocarboxylic acid, other monocarboxylic acids, dicarboxylic acid, malic acid, thiodicarboxylic acid, tartaric acid, malonic acid, other dicarboxylic acids, polyvalent carboxylic acid, sugars, tetrafluoroborate, phosphoric acids, sulfonic acids, hydrocarbon, acid salts of amines, and acid salts of aromatic amines. In one example, the acid preferably has a pH of 2.0 or more from the viewpoint of tissue damage.

More specific examples of the acid include compounds shown in Table. 4. Examples of preferable acids among the compounds shown in Table. 4 include a compound having a Score value of not more than 0.9 in the Examples. Examples of more preferable acids among the compounds shown in Table. 4 include #1165 and #1300. The acid may be of a single kind or of two or more kinds.

In one example, the base is preferably a compound having a delipidation removal ability. Specific examples of the base include bases (amine, aminoalcohol, and pyridine) having the delipidation removal ability described in (A) above. In particular, aminoalcohol is preferable, and #0414 and an analog thereof are more preferable. Examples of the analog of #0414 include N-alkyl dialcoholamine. The alkyl group of the N-alkyl dialcoholamine may be linear, branched, or cyclic. The alkyl group of the N-alkyl dialcoholamine may be saturated or unsaturated. The number of carbon atoms constituting the alkyl group of the N-alkyl dialcoholamine is not particularly limited, and, for example, the number may be 1 to 8, and is 4 in a preferable example. The two alcohol moieties may each have any number of carbon atoms, and the number may be the same or different between the two alcohol moieties. For example, the number may be 1 to 8, and is two in a preferred example. The base may be of a single kind or of two or more kinds.

In another example, the base is preferably an imidazole analog, more preferably #1352. Other preferable examples of the base include a heterocyclic amine such as #1278 (4-methylmorpholine), and #0370 (2-amino-6-methylpyridine).

A solution containing (C) has a pH which is preferably 6 to 11, more preferably 7 to 9, and further more preferably approximately 8.

The concentration of the EDTA in the solution containing (C) is not particularly limited, and is preferably 5 wt % to 25 wt %, more preferably 7.5 wt % to 20 wt %, and further more preferably approximately 10 wt %. The concentration of the acid in the solution containing (C) is not particularly limited, and is preferably 5 wt % to 25 wt %, more preferably 7.5 wt % to 20 wt %, and further more preferably approximately 10 wt %. The concentration of the base in the solution containing (C) is not particularly limited, provided that the solution has a target pH level. In one example of a method for preparing the solution containing (C), the base is added to a solution which contains the EDTA and the acid.

((D) Compound Having Refractive Index Adjusting Ability)

A compound (D) which may be contained in the composition in accordance with the present invention is a compound having a refractive index adjusting ability. In one example, the compound (D) has a high refractive index adjusting ability.

In one embodiment, the compound (D) is a compound which is soluble at a concentration of 60 wt % or more in water and which allows an aqueous solution, in which the compound (D) is contained at a concentration that is at least one value within a range of 60 wt % to 80 wt %, to have a refractive index of 1.47 to 1.50.

In another embodiment, the compound (D) is at least one of, for example, a benzylamine, a pyridine, an amine, a benzylaminoalcohol, hydrazine, and thiourea.

More specific examples of the compound (D) include compounds shown in Table. 3 and analogs thereof. From the viewpoint of preventing shrinkage, the compound (D) is preferably a salt-free compound. Examples of such a compound include #0370, #0389, #0587, #0609, #0640, #1102, and #1283 shown in Table. 3 and analogs thereof. Among these compounds, from the viewpoint of achieving a higher transparency, #0587, #0640, #1102, #1283 and analogs thereof are preferable, and #0587 and an analog thereof is more preferable.

Among the compounds shown in Table. 3 and analogs thereof, #0640, #0450, #1283, #0864, #1052, #0788, #0389 and analogs thereof are preferable from the viewpoint of allowing retention of fluorescence of a fluorescent protein.

Further, from the viewpoint of achieving a higher transparency, a combination of #0640 and #1283, a combination of #0640 and nicotinamide (#0855), and a combination of Histodenz and #1283 are also preferable.

The compound (D) may be of a single kind or of two or more kinds.

In one example, the concentration of the compound (D) in the composition is preferably a concentration which allows the composition to have a refractive index of 1.47 to 1.53. Specifically, for example, the concentration (in a case where the composition contains two or more compounds, the total concentration of these compounds) is preferably 50 wt % to 90 wt %, more preferably 60 wt % to 85 wt %, and further more preferably 70 wt % to 80 wt %. With respect to the specific combinations described above, for example, it is preferable that the concentration of the former one of each combination be 40 wt % to 50 wt %, and the concentration of the latter one of the each combination be 25 wt % to 35 wt %.

((E) Compound Having Tissue Swelling Ability)

A compound (E) which may be contained in the composition in accordance with the present invention is a compound having a tissue swelling ability. In one example, the compound (E) has a high tissue swelling ability.

In one embodiment, the compound (E) is a compound exhibiting a swelling activity higher than that of urea. The swelling activity may be measured, for example, by a method described in the Examples.

Examples of the compound (E) include compounds shown in FIG. 20 , imidazole derivatives, and antipyrine analogs.

The compound (E) may be of a single kind or of two or more kinds.

The concentration of the compound (E) in the composition is not particularly limited, and, for example, the concentration (in a case where the composition contains two or more compounds, the total concentration of these compounds) is preferably 5 wt % to 40 wt %, more preferably 5 wt % to 30 wt %, and more preferably 5 wt % to 25 wt %.

In one example, the compound (B) is capable of swelling a biological material so as to increase the volume of the biological material by 4 times to 10 times, while maintaining the shape of the biological material.

(Combination)

Two or more of (A) to (E) may be contained in a single composition.

In one example, the composition preferably contains at least one of (A) and (E) as an essential component. In a case where a biological material contains plenty of blood or a biochrome such as myoglobin, the composition preferably contains (B). In a case where a biological material contains bone tissue, the composition preferably contains (C).

(Solvent)

A solvent for use in the composition in accordance with the present invention is not limited to any particular kind, as long as the solvent allows the above-described active ingredients to be dissolved therein. Preferably, water is used as a main solvent; particularly preferably, only water is used as the solvent. Note that, in the present invention, what is meant by the expression “water is used as a main solvent” is that the volumetric percentage of water with respect to all solvents used is larger than that of any other solvent, and preferably that water is used in an amount that accounts for more than 50% and not more than 100% of the total volume of all solvents used. The composition in accordance with the present invention, in a case where the composition is prepared with use of water as a main solvent, is referred to as a “reagent in the form of an aqueous solution”.

In the case where water is used as a main solvent, dimethyl sulfoxide (DMSO) may be mixed with the water for application to a fixed sample, for example. It is expected that, for example, use of a mixture of DMSO and water to a fixed sample provides effects such as (i) improvement in permeability of the reagent with respect to a biological material and (ii) facilitation of a clearing treatment with respect to a tissue having a keratin surface.

Main advantages of the use of water as the solvent are as follows:

1) The active ingredients of the composition in accordance with the present invention are excellent in solubility in water; therefore, the use of water as the solvent makes it possible to (i) inexpensively prepare the composition in accordance with the present invention and (ii) easily prepare the composition in accordance with the present invention.

2) Compared with a case where an organic solvent is used as a main solvent, the use of water as the solvent does not involve dehydration of a biological material when the biological material is subjected to a clearing treatment; therefore, the use of water as the solvent can prevent the problem of shrinkage of a biological material.

3) Compared with a case where an organic solvent is used as a main solvent, the use of water as the solvent significantly reduces the possibility of damaging a fluorescent protein; this makes it possible to observe, with use of a fluorescent protein, a biological material having been subjected to a clearing treatment.

4) The use of water as the solvent makes it possible to apply the composition in accordance with the present invention not only to a clearing treatment on a fixed material but also to a clearing treatment on a living material.

5) The use of water as the solvent makes a clearing treatment reversible, that is, the use of water as the solvent can as necessary bring a biological sample having been subjected to a clearing treatment back to a state that it had before the clearing treatment.

6) Compared with a case where an organic solvent is used as a main solvent, the use of water as the solvent enhances safety in handling of the composition in accordance with the present invention.

The composition in accordance with the present invention may be a buffer solution that can maintain a pH suitable for a biological material to be subjected to a clearing treatment. Further, the composition in accordance with the present invention may have an osmotic pressure adjusted to such a degree that no deformation is caused of a biological material to be subjected to a clearing treatment and that the active ingredients sufficiently penetrate into the biological material.

(Other Optional Components)

A solution as the composition in accordance with the present invention may contain an optional component as necessary. Examples of the optional component include a pH adjusting agent, an osmotic pressure controlling agent, and the like.

[2. Method]

The present invention provides a method for preparing a biological material having an excellent light-transmitting property. A method in accordance with the present invention is characterized by including the step of: permeating (permeation step) into a biological material a solution containing at least one (one, two, three, four, or five) of the above-described (A) to (E). The solution is as described above.

In one embodiment, the method in accordance with the present invention may include the steps of: permeating (first permeation step) into a biological material a solution (first solution) containing at least one of (A) to (E); and permeating (second permeation step) into the biological material a solution (second solution) containing at least another one of (A) to (E), and may further include at least one (one, two, three, four, or five) of the steps of: permeating (third permeation step) into the biological material a solution (third solution) containing at least still another one of (A) to (E); permeating (fourth permeation step) into the biological material a solution (fourth solution) containing at least still another one of (A) to (E); and permeating (fifth permeation step) into the biological material a solution (fifth solution) containing at least still another one of (A) to (E).

(Permeation Step)

In the permeation step, at least one of: delipidation with use of the compound (A); decoloring with use of the compound (B); decalcification with use of the compound (C); refractive index adjustment with use of the compound (D); and swelling with use of the compound (E) is performed. That is, the method in accordance with the present invention includes at least one (one, two, three, four, or five) of a delipidation step with use of the compound (A), a decoloring step with use of the compound (B), a decalcification step with use of the compound (C), a refractive index adjustment step with use of the compound (D), and a swelling step with use of the compound (E). In a case where the method includes a plurality of steps, the steps may be carried out separately, or two or more of the steps may be carried out simultaneously.

A biological material which has been subjected to the delipidation step exhibits an excellent light-transmitting property due to removal of a light scattering substance (mainly lipids) in the biological material. Accordingly, the delipidation step is particularly effective for a case in which a lipid-rich biological material (e.g., a lipid-rich organ or tissue) is made transparent. The delipidation step may be performed, for example, at 25° C. to 45° C. for approximately 1 day to 10 days.

A biological material which has been subjected to the decoloring step exhibits an excellent light-transmitting property due to decoloring of biochromes (mainly hemoglobin in blood) in the biological material. Accordingly, the decoloring step is particularly effective for a case in which blood is made transparent and for a case in which a blood-rich biological material (e.g., a blood-rich organ or tissue) is made transparent. The decoloring step may be performed, for example, at 25° C. to 45° C. for approximately 1 day to 5 days.

A biological material which has been subjected to the decalcification step exhibits an excellent light-transmitting property due to decalcification of calcium-rich tissue (bones, teeth, etc.) in the biological material. Accordingly, the decalcification step is particularly effective for a case in which a calcium-rich biological material (e.g., a calcium-rich organ or tissue) is made transparent. The decalcification step may be performed, for example, at 25° C. to 45° C. for approximately 3 days to 10 days.

A biological material which has been subjected to the refractive index adjustment step exhibits an excellent light-transmitting property due to a reduced difference between a refractive index of a liquid component and a refractive index of biomolecule such as a protein. Accordingly, the refractive index adjustment step is effective for any biological material. The refractive index adjustment step may be performed, for example, at 25° C. to 37° C. for approximately 1 day to 4 days.

A biological material which has been subjected to the swelling step is swollen, and accordingly exhibits an excellent light-transmitting property. Further, the biological material is observable with an improved optical resolution. The swelling step therefore is effective for any biological material. The swelling step may be performed, for example, at 10° C. to 35° C. for approximately 1 day to 7 days.

The order in which the steps are carried out is not particularly limited, but in a case where all of the five steps are carried out, the five steps are preferably carried out in the order of (1), (2), and (3) below.

(1) Delipidation step, decoloring step (2) Decalcification step, swelling step (3) Refractive index adjustment step

In (1), the delipidation step and the decoloring step may be carried out separately or simultaneously. In one example, the compound (A) to be used in the delipidation step and the compound (B) to be used in the decoloring step are partially or entirely identical to each other, and the delipidation step and the decoloring step can thus be carried out simultaneously. Alternatively, the delipidation step and the decoloring step may be carried out simultaneously by using a mixture of the compound (A) and the compound (B). In a case of separately carrying out the delipidation step and the decoloring step, either of the delipidation step and the decoloring step may be carried out first, but it is preferable to carry out the delipidation step first. In (2), the order in which the decalcification step and the swelling step are carried out is not particularly limited, and either one of the decalcification step and the swelling step may be carried out first.

Also in a case where at least one of the five steps is not carried out, it is preferable to carry out the other ones of the five steps in the above-described order.

(Other Optional Steps)

The method in accordance with the present invention may include the step of: washing (washing step) of washing a biological material at given timing. The washing step may be carried out at timing such as, for example, before a permeation step, between permeation steps, and/or after completion of a permeation step. The washing may be carried out with use of PBS, distilled water, or the like. The washing may be carried out, for example, 1 to 5 times per washing step.

In the method in accordance with the present invention, a biological material which has been made transparent may be preserved at given timing, for example, in a room temperature or low temperature environment (cleared sample preservation step). In such a case, in order to prevent drying of the biological material, the biological material is preferably preserved in a state where the biological material is immersed in the solution or an equilibrated salt solution such as PBS.

The method in accordance with the present invention may be combined with a clearing method other than the method in accordance with the present invention. For example, it is possible to carry out the delipidation step and the decoloring step in accordance with the method of the present invention and carry out refractive index adjustment in accordance with a clearing method (e.g., SeeDB method) other than the clearing method of the present invention.

On a biological material having been made transparent, a step of observation (observation step) with use of, for example, an optical microscope is performed. On a biological material to be subjected to the observation step, a visualizing treatment step such as staining or marking may as necessary be performed (i) before the clearing treatment of the present invention or (ii) after the clearing treatment and before the observation step. For example, in a case where the visualizing treatment step involves use of a fluorescent protein, a fluorescent protein gene is introduced into a living biological material before the clearing treatment so that the fluorescent protein will be expressed therein. In a case where the visualizing treatment step is (i) injection of fluorescent chemical (small) molecules (which is not a fluorescent protein) into a biological material or (ii) staining of a biological material with use of fluorescent chemical (small) molecules, the visualizing treatment step is preferably performed before the clearing treatment. However, the visualizing treatment step may be performed after the clearing treatment. Alternatively, the visualizing treatment step may be staining of a biological material with use of a chemical substance which is not fluorescent chemical molecules.

The observation step can be performed with use of any type of optical microscope. For example, the observation step can be performed with use of a light-sheet microscope, a two-photon laser microscope, a confocal microscope, and/or the like. The method in accordance with the present invention is particularly suitably applicable to a high-throughput analysis of multiple samples at a low-magnification.

[3. Kit]

The present invention provides a kit which includes a composition for preparing a biological material having an excellent light-transmitting property.

The term “kit” as used in the present specification refers to a package including a container (for example, a bottle, a plate, a tube, a dish, or the like) containing a particular material (for example, a constituent component). The kit is preferably provided with a manual for use of each material. Various forms of the verb “include” as used in the present specification to describe an aspect of the kit refer to a state in which the material is contained in any of the individual containers constituting the kit. A kit in accordance with the present invention may be a single package containing a plurality of different compositions. The compositions may each be contained in one of a plurality of different containers in a case where the compositions are each in the form of a solution. The kit in accordance with the present invention may include its constituent elements either (i) in a single container as the constituent elements are mixed with each other or (ii) in separate containers. The “manual” may be printed or written on a medium such as paper or an electronic medium such as a magnetic tape, a computer-readable disc or tape, or a CD-ROM. The manual shows a procedure for achieving the purpose of the kit. The kit in accordance with the present invention may further include a container containing a diluent, a solvent, a cleaning fluid, or another reagent. In addition, the kit in accordance with the present invention may include an instrument and a reagent that are necessary to carry out the procedure for achieving the purpose of the kit.

In one example, the kit may include two or more kinds of the above-described composition. For example, in a case of performing the delipidation step and the decoloring step separately, the kit may include a composition containing (A) and a composition containing (B). In one embodiment, the kit includes at least two (two, three, four, or five) of a composition containing (A), a composition containing (B), a composition containing (C), a composition containing (D), and a composition containing (E). In another embodiment, the kit includes at least (i) a composition containing at least two (two, three, four, or five) of (A) to (E) and (ii) a composition containing at least another one (one, two, three, four, or five) of (A) to (E).

The following will provide Examples to more specifically describe embodiments of the present invention. As a matter of course, the present invention is not limited to Examples provided below, and details of the present invention can be realized in various manners. Further, the present invention is not limited to the embodiments described above, and it may be varied in various ways within the scope of the appended claims. Thus, an embodiment based on a proper combination of technical means disclosed in different embodiments is encompassed in the technical scope of the present invention. In addition, the present specification encompasses the contents of the specification and/or drawings of Japanese Patent Application No. 2016-092025, to which the present application claims priority. Furthermore, all of the publications and patents cited in the present specification are incorporated herein by reference in their entirety.

EXAMPLES

[1. Search for Clearing Reagent]

An experiment technique was developed for high-throughput evaluation of a library of 1619 water-soluble compounds to identify a good compound in terms of each of the following five parameters that are required in clearing: (A) delipidation ability, (B) biochrome decoloring ability, (C) decalcification ability, (D) refractive index adjusting ability, and (E) tissue swelling ability.

(A. Delipidation Ability)

The library of 1619 water-soluble compounds was screened for compounds having a delipidation ability, with use of an assay method involving solubilization of fixed brain tissue described in Susaki et al., Cell, 157, 726-739, 2014.

Specifically, brains taken out of mice were sheared with a utility knife and then were disrupted by ultrasonication. To each of the resultant suspensions, an equal volume of 8% PFA solution was added to perform fixation at 4° C. for 1 hour. The resultant mixture was centrifuged to remove the supernatant, and the fixed brain tissue was washed with PBS for 3 times. PBS was added so as to obtain 2 mL of a fixed brain tissue suspension per brain. The fixed brain tissue suspension was diluted by 3.5 folds. To 20 μL of the resultant suspension, 130 μL of each 10 wt % chemical was added and was shaken at 37° C. overnight. Thus obtained mixed solutions were subjected to absorbance (turbidity) measurement at 600 nm. It is expected that a chemical solution which reduces the turbidity of a fixed brain suspension allows reducing light scattering by solubilizing lipids, which act as a scattering factor, in the brain tissue. Top 50 chemicals contributing to turbidity reduction were categorized by chemical properties, and it was thus revealed that detergents, aminoalcohols, aliphatic amines, and pyridines were effective (Table. 1, FIG. 1 ). Further, the reduction in turbidity of a fixed brain suspension was correlated with the pH of the solution, and the reduction in turbidity was more significant as the basicity of the solution increased (FIG. 2 ).

Subsequently, the delipidation efficiency of the series of compounds in mammalian tissue was examined. A mouse hemisphere was treated with use of each 10 wt % chemical solution at 37° C. for 3 days, washed with PBS, and then subjected to refractive index adjustment with CUBIC-2A (22.5 wt % sucrose, 22.5 wt % antipyrine, 25 wt % urea, and 10 wt % triethanolamine). The transmittance of the brain tissue was measured, and then the brain tissue was washed with PBS and was disrupted. The lipid content (phospholipid content and cholesterol content) of the resultant suspension was quantified (FIG. 3 ), in which a close correlation between a residual phospholipid content and tissue transmittance was observed (FIG. 4 ). This indicates that the lower the phospholipid content is, the higher the tissue transparency is. This result directly verifies that delipidation contributes to transparency. Importantly, as compared with the detergents typified by #1035, #1455, #1460, and Triton X-100, higher degrees of delipidation and clearing were observed with basic chemicals such as aminoalcohols and aliphatic amines and with some neutral chemicals such as #1051. It was thus shown that the above basic chemicals and some neutral chemicals were better than the detergents from the viewpoint of permeability with respect to tissue. Among the obtained basic chemicals, #0070 (1,3-bis(aminomethyl)cyclohexane) was selected from the viewpoint of price and odor of a reagent.

A study was conducted to identify a combination of #0070 and another chemical which combination would synergistically contribute to delipidation so as to maximize delipidation activity (FIG. 5 ). A small piece of human brain white matter was treated with use of a cocktail of 10 wt % #0070+each 10 wt % chemical at 37° C. for 4 days. The small piece was washed with PBS and then subjected to refractive index adjustment with CUBIC-2A. It was thus revealed that a combination of #0070 and SDS, which is a detergent, was the best from the viewpoint of allowing high-level clearing without damage to tissue.

Further, in order to search for an optimal detergent, various cocktails of 10 wt % #0070+10 wt % detergent were prepared and compared with each other in terms of clearing of human brain white matter (FIG. 6 ). It was thus revealed that a cocktail of 10 wt % #0070+10 wt % #0631 is an optimal combination.

It was shown that fluorescence of EGFP, which is a typical fluorescent protein, is quenched at a pH of 12 or more at 37° C. (FIG. 7 ). As such, only those basic chemicals which had a pH of 11 to 12 were subjected to comparison in terms of transparency of mouse hemispheres (FIG. 8 ). A mouse hemisphere was treated with use of each 10 wt % chemical solution at 37° C. for 3 days, and was washed with PBS. Subsequently, the mouse hemisphere was subjected to refractive index adjustment with CUBIC-2A. From results obtained, #0389 and #0414 were selected. However, various studies which were thereafter conducted showed superiority of #0414 in terms of organ transparency. Accordingly, #0414 (N-butyldiethanolamine) was selected as a highly-efficient delipidation chemical.

Subsequently, a study was conducted to identify a combination of #0414 and another chemical which combination would synergistically contribute to delipidation so as to maximize delipidation activity (FIG. 9 ). A mouse kidney was treated with use of a cocktail of 10 wt % #0414+each 10 wt % chemical at 37° C. for 1 day, washed with PBS, and then subjected to refractive index adjustment with CUBIC-2A. It was thus revealed that a combination of #0414 and Triton X-100 is optimal in terms of both delipidation activity and transparency. It was also revealed that the cocktail of #0414+Triton X-100 does not induce quenching of EGFP (FIG. 10 ). A mouse whole brain was treated with use of a cocktail of 10 wt % #0414+10 wt % Triton X-100 at 37° C. for 3 days, washed with PBS, and then subjected to refractive index adjustment with CUBIC-2A. It was thus confirmed that the cocktail of #0414+Triton X-100 yields significant improvements in transparency and delipidation efficiency as compared with a conventional CUBIC-1 reagent (FIG. 11 ).

(B. Biochrome Decoloring Ability)

A high-throughput screening system for evaluating the decoloring ability of various compounds was constructed. The screening system involved adding an aqueous solution of each compound to bovine coagulated blood and then measuring the absorbance of heme collected in the supernatant. The screening system was used to screen the library of 1619 water-soluble compounds for a compound having a biochrome decoloring ability.

Specifically, to bovine blood, an equal amount of 8% PFA solution was added, and reacted at 4° C. overnight. The mixed liquid was centrifuged at 1500×g for 5 minutes, and the supernatant containing PFA was discarded. Then, the same amount of PBS as the original volume of blood was added to prepare a coagulated blood sample. To 150 μL of 10 wt % aqueous solution of each compound, 50 μL of the coagulated blood sample was added, and reacted at 37° C. overnight. The reaction solution was centrifuged at 1500×g for 5 minutes, and then 100 μL of the supernatant was added to a plate so as to be subjected to absorbance measurement. A sample which is suspended in water instead of being dissolved in the water has a weak decoloring effect, but none the less has a high absorbance value. In view of this, the OD720 and OD420 of the supernatant were measured as a scattering index and a heme elution index, respectively. OD420-OD700 was defined as decoloring activity of each chemical, and chemicals exhibiting a decoloring activity higher than that of an aminoalcohol (N,N,N′,N′-tetrakis(2-hydroxypropyl)ethylenediamine), which had been already known to exhibit a decoloring activity, were identified (Table. 2). This screening allowed identifying, as a group of compounds having a notably high decoloring activity, (i) detergents typified by alkyl imidazole and a salt of pyridinium and (ii) bases such as alkylamine.

In order to examine the decoloring efficiency of the series of compounds in mammalian tissue, a mouse spleen was treated at 37° C. overnight with use of 10 wt % solution of each chemical which solution would not induce quenching of EGFP. Subsequently, the OD420 of the supernatant was measured, and a transmissive image of the organ was captured (FIG. 12 ). The results showed that #0938 (1-ethylimidazole) had the highest mouse spleen decoloring activity. Since this reagent is expensive (176 yen per gram), 1-methylimidazole (25.8 yen per gram) was selected as an alternative having an equivalent decoloring activity. In hemoglobin, heme is coordinate-bonded to oxygen and histidine. 1-alkyl imidazole has a skeleton similar to that of histidine, and is thus assumed to have high affinity for heme. This seems to be a factor that allowed the 1-alkyl imidazole to exhibit a high decoloring activity. Meanwhile, little decoloring activity was observed with respect to imidazoles whose nitrogen atom at the position 1 was not alkylated. It is thus understood that alkylation of a nitrogen atom at the position 1 improves affinity for heme.

(C. Decalcification Ability)

For comprehensive screening of the library of 1619 water-soluble compounds for a compound having a decalcification activity, a screening system involving use of hydroxyapatite, which is a main component of bone tissue, was constructed. Hydroxyapatite (200 mg/mL) was suspended in 40 v/v % glycerol, and mixed with an aqueous solution of each compound. Then, the turbidity of the mixed solution was measured. Specifically, 20 μL of a 200 mg/mL hydroxyapatite-40 v/v % glycerol suspension was dispensed to each well of a 96-well plate reader. 130 μL of each reagent was added to the well, and was shaken and stirred at 37° C. overnight. Then, the OD600 of each mixture was measured to evaluate the decalcification activity of the mixture. With respect to an OD600 value (defined as score 1.0) obtained in a case where the treatment was performed with use of water, the score of each compound aqueous solution was calculated. The closer the score of a chemical is to 0, the higher the decalcification activity of the chemical is. Decalcification is commonly known to progress quickly in the presence of a strong acid such as hydrochloric or nitric acid. Under such a condition, it is not possible to observe signals of a fluorescent protein. Meanwhile, EDTA, which is in a neutral range, allows maintaining signals of a fluorescent protein. However, EDTA has a decalcification ability lower than those of strong acids, and thus requires long hours of decalcification operation. Development was conducted in the present invention to obtain a solution which would exhibit a significant decalcification activity when combined with the EDTA in the neutral range. Screening results showed that most of the compounds having a pH of less than 2.0 had a score 0. Accordingly, a group of compounds having a pH of 2.0 or more is listed in Table. 4, in which the compounds are sorted in accordance with characteristics of their structure formulae. Among the group of compounds, those compounds having a low score are shown in boxes.

In order to examine whether or not these compounds are effective for decalcification, a cocktail was prepared by neutralizing a mixed solution of 10 wt % EDTA+each 10 wt % decalcification-candidate compound to a pH of 7 to 8 with use of a solution of #0070, which had been found to be useful as a delipidation reagent. A mouse femur was treated with use of (i) an EDTA-Na solution with a pH adjusted to 7 to 8 using NaOH or (ii) an EDTA—each decalcification candidate compound—#0070 solution. Then, a change in transmittance of the femur was measured (this experiment was conducted twice independently). It was thus discovered that the EDTA—decalcification candidate compound—#0070 solutions exhibited a significantly improved decalcification activity as compared with the conventional EDTA-Na solutions (FIG. 13 ). Further, no quenching of GFP was observed. From the results of FIG. 13 , it was revealed that an EDTA—#1165-#0070 solution and an EDTA—#1300-#0070 solution were the most effective decalcification reagents.

Subsequently, an attempt was made to study how to optimize the basic chemical which had been used for the pH adjustment. Since an experimental system using a femur would create significant experimental errors, an evaluation system using hydroxyapatite was used in the study in order to conduct more detailed optimization of the decalcification activity of EDTA. Specifically, 20 μL of a 60 mg/mL or 200 mg/mL hydroxyapatite-40 v/v % glycerol suspension was dispensed to each well of a 96-well plate reader. 130 μL of each reagent was added to the well, and was shaken and stirred at 37° C. overnight. Then, the OD600 of each mixture was measured to evaluate the decalcification activity of the mixture. A cocktail was prepared by neutralizing 10 wt % EDTA to a pH of approximately 8 with use of a basic amine typified by #0070, #0390, #0414, #1027, #1439, and #1456, which had been found to be useful as a delipidation reagent. The evaluation conducted with use of the prepared cocktails showed that 10 wt % EDTA—#0414 exhibited the most effective decalcification action (FIG. 14 ).

With respect to a cocktail obtained by neutralizing 10 wt % EDTA with use of #0414 (EDTA—#0414) and a cocktail obtained by neutralizing 10 wt % #0414 with use of EDTA (#0414—EDTA), pH dependency of the decalcification activity of these cocktails was examined. Remarkably higher decalcification activities of these cocktails as compared with those of conventional EDTA-NaOH solutions were confirmed at a pH of approximately 8 (FIG. 15 ). Studies of temperature dependency and EDTA concentration dependency showed that (i) the decalcification activity increased as the temperature increased and (ii) the decalcification activity was maximized at an EDTA concentration of approximately 10 wt % (FIG. 16 ). On the basis of these conditions, clearing was conducted on a mouse femur, around which tissues had been dissolved with use of sodium hydrate. Efficient progress of decalcification was observed in the clearing.

Further, comprehensive search for a basic chemical was conducted with use of an evaluation system involving use of hydroxyapatite. Specifically, 20 μL of a 150 mg/mL hydroxyapatite-40 v/v % glycerol suspension was dispensed to each well of a 96-well plate reader. 130 μL of each reagent was added to the well, and was shaken and stirred at 37° C. overnight. Then, the OD600 of each mixture was measured to evaluate the decalcification activity of the mixture. A cocktail was prepared by neutralizing 10 wt % EDTA to a pH of approximately 8 with use of a basic chemical having a pH of 11 or more. With use of the prepared cocktail, a decalcification treatment was conducted (FIG. 17 ). Comparison of relative decalcification activities showed that imidazole analogs had decalcification activities superior to those of the other categories. In particular, a cocktail neutralized by #1352 (imidazole) exhibited the highest decalcification. Also, a cocktail neutralized by #1278 (4-methylmorpholine), which is a heterocyclic amine, and a cocktail neutralized by #0370 (2-amino-6-methylpyridine) having a pyridine skeleton, exhibited high decalcification activities.

(D. Refractive Index Adjusting Ability)

The refractive index of an aqueous solution is commonly known to increase in a solute concentration-dependent manner, and the refractive index of a reagent per unit weight of the reagent varies among individual reagents. Accordingly, two properties are required in order to prepare a high refractive index aqueous solution: (1) an extremely high water-solubility and (2) a solvent which allows achieving a high refractive index in a low-concentration aqueous solution. In order to conduct a comprehensive search of the library of 1619 water-soluble compounds for a reagent satisfying the above (2), the refractive index at 589 nm of 10 wt % aqueous solution of each compound was measured so as to screen for compounds having a high refractive index. In order to further select a compound having a high water-solubility from among these compounds, 60 wt % to 80 wt % aqueous solution was prepared, and a group of compounds having a refractive index of 1.47 to 1.50 was identified (Table. 3).

From the viewpoint of preventing shrinkage, a comparison was made of 7 salt-free compounds among the group of compounds in terms of refractive index adjusting effect. Specifically, a kidney of an 8-week old male mouse was shaken in a 10 wt % #0414+10 wt % Triton X-100 mixed solution at 37° C. for 4 days, and then washed with PBS. Further, the kidney was shaken in a 2-fold diluted high refractive index solution at 37° C. overnight. Subsequently, the kidney was further shaken in an undiluted high refractive index solution at 37° C. overnight. Then, a transmissive image of the kidney was captured, and the transmittance of tissue of the kidney was measured (FIG. 18 ). Note that CUBIC-2A solution, 70 wt % Histodenz solution, and 70 wt % sucrose solution were used as controls. The measurement results showed that, as compared with the high-concentration Histodenz solution and the high-concentration sucrose solution which had been already reported, #0587, #0640, #1102, and #1283 achieved better results in terms of both the appearance and transmittance of the organ.

Subsequently, in order to search for high-level refractive index adjusting agents with use of cocktails of these chemicals, various 46 wt %/30 wt % mixed solutions were prepared. A lung of an 8-week old male mouse was shaken in a 10 wt % #0414+10 wt % Triton X-100 mixed solution at 37° C. for 4 days, and then washed with PBS. Further, the lung was shaken at 37° C. overnight in a 2-fold diluted high refractive index solution. Subsequently, the lung was further shaken in an undiluted high refractive index solution at 37° C. overnight. Then, a transmissive image of the lung was captured, and the transmittance of tissue of the lung was measured (FIG. 19 ). The measurement results showed that all of the cocktails achieved good transparency, and particularly a cocktail of 46 wt % #0640+30 wt % #1283, a cocktail of 46 wt % #0640+30 wt % nicotinamide (#0855), and a cocktail of 46 wt % Histodenz+30 wt % #1283 had the highest transparencies.

(E. Tissue Swelling Ability)

It is commonly known that causing tissue to swell allows increasing the transparency of the tissue. A high correlation between a swelling-shrinking behavior of a brain and a swelling-shrinking behavior of gelatin was confirmed, and a screening system involving use of gelatin was established. 9% gelatin aqueous solution and 0.8% paraformaldehyde solution were mixed together. 200 μL of the mixed solution was dispensed to each well of a 96-well plate, and then incubated at 4° C. for 16 hours. To the gelatin plate thus gelated, 170 μL of 10 wt % aqueous solution of each compound from the library of 1619 water-soluble compounds was dispensed, and was incubated at room temperature for 72 hours. Then, the gelatin plate was washed with use of pure water approximately 3 times. The water was thoroughly wiped off, and the absorbance of the gelatin at 975 nm, which is one of the absorption wavelengths of water, was measured. The library of 1619 water-soluble compounds was screened for a group of compounds each having a swelling activity score higher than that (score 1) of urea. As a result, water-soluble compounds having a swelling activity were identified (FIG. 20 ).

In order to verify that the identified compounds actually had an activity of swelling a mouse brain, a brain which had been subjected to a delipidation treatment with use of CUBIC-1 was shaken, in a solution containing #1352 among the compounds, for 3 days while replacing the liquid every 12 hours. As a result, a high-degree of swelling was observed (FIG. 21 ). Further, in order to verify that the swollen brain actually exhibits high transparency, the brain which had been swollen with use of #1352 was shaken in a 55 wt % #0640+5 wt % #1352 mixed solution which had a high refractive index adjusting ability. A brain sample which had very high transparency while in a swollen state was successfully produced (FIG. 22 ).

[2. Example Use of Clearing Reagent]

(1. Clearing of Mouse Liver and Tissue Including Human Brain White Matter)

Clearing of a mouse liver and tissue including human brain white matter can be performed, for example, in accordance with the following procedure.

(1) A liver of a mouse which has been subjected to perfusion fixation with use of 4% paraformaldehyde solution or human brain tissue which has been fixed with use of formalin is immersed in PBS.

(2) The mouse liver or the human brain tissue is immersed in a permeabilization solution (Sol. PE: 10 wt % 1,3-bis(aminomethyl)cyclohexane, 10 wt % sodium dodecylbenzenesulfonate or sodium dodecyl sulfate) at 37° C. for 2 days to 4 days.

(3) The mouse liver or the human brain tissue is washed with PBS several times for several hours per washing.

(4) The mouse liver or the human brain tissue is immersed in a clearing solution (Sol. CL: 22.5 wt % sucrose, 22.5 wt % antipyrine, 10 wt % triethanolamine, 25% urea) at 50° C. for approximately 2 days to 4 days.

(5) The mouse liver or the human brain tissue is washed with PBS again as necessary, and preserved.

Results of clearing actually performed in accordance with the above procedure are shown in FIG. 23 .

(2. Decoloring of Mouse Spleen)

Decoloring of a mouse spleen can be performed, for example, in accordance with the following procedure.

(1) Spleen tissue of a mouse which has been subjected to perfusion fixation with use of a 4% paraformaldehyde solution is immersed in PBS.

(2) The spleen tissue is immersed in 10 wt % #0441 (benzethonium chloride), #0484 (1-(3-aminopropyl)imidazole), #0651 (decyldimethyl(3-sulfopropyl)ammonium hydroxide intramolecular salt), #0938 (1-ethylimidazole), or #1283 (N-methylnicotinamide) at 37° C. for approximately 2 days to 4 days. As controls, spleen tissue is immersed in #10 (N,N,N′,N′-tetrakis(2-hydroxypropyl)ethylenediamine), CUBIC-1, or PBS at 37° C. for approximately 2 days to 4 days.

(3) An image of each spleen tissue thus decolored is captured. Heme eluted into a supernatant is quantified by measuring the absorbance of the spleen at 420 nm.

Results of decoloring actually performed in accordance with the above procedure are shown in FIG. 12 .

(3. Clearing of Mouse Brain Tissue)

Clearing of mouse brain tissue can be performed, for example, in accordance with the following procedure.

(1) Brain tissue of a mouse which has been subjected to perfusion fixation with use of 4% paraformaldehyde solution is immersed in PBS, and cut into brain hemispheres.

(2) Each brain hemisphere is immersed in a brain delipidation solution (10 wt % N-butyldiethanolamine, 10 wt % Triton X-100) at 37° C. for approximately 2 days to 4 days.

(3) The brain hemisphere is washed with PBS several times for several hours per washing.

(4) The brain hemisphere is immersed in a clearing solution (Sol. CL: 22.5 wt % sucrose, 22.5 wt % antipyrine, 10 wt % triethanolamine, 25% urea) at 37° C. for approximately 1 day.

(5) The brain hemisphere is washed with PBS again as necessary, and preserved.

A result of clearing actually performed in accordance with the above procedure is shown in FIG. 24 .

(4. Adjustment of Refractive Index of Delipidated Tissue)

Adjustment of the refractive index of delipidated tissue can be performed, for example, in accordance with the following procedure.

(1) Brain tissue of a mouse which has been subjected to perfusion fixation with use of 4% paraformaldehyde solution is subjected to post-fixation with use of 4% paraformaldehyde solution. Then, the mouse brain tissue is immersed in PBS, and cut into brain hemispheres.

(2) Each brain tissue thus cut is immersed in CUBIC-1 at 37° C. for approximately 3 days to 5 days.

(3) The brain tissue is immersed in PBS for approximately 1 day.

(4) The brain tissue is immersed in 70 wt % #0389 (N-benzylethanolamine), 60 wt % #0640 (antipyrine), or 70 wt % #0788 (N,N-dimethylbenzamide) at room temperature for approximately 1 day.

Results of refractive index adjustment actually performed in accordance with the above procedure are shown in FIG. 25 .

(5. Clearing of Various Mouse Organs)

Clearing of various organs (brain, heart, lung, liver, and kidney) of a mouse can be performed, for example, in accordance with the following procedure.

(1) An organ of a mouse which has been subjected to perfusion fixation with use of 4% paraformaldehyde solution is taken out, and subjected to post-fixation with use of 4% paraformaldehyde solution at 4° C. overnight.

(2) The mouse organ is washed with PBS several times for several hours per washing.

(3) The mouse organ is immersed in a permeabilization CUBIC-L solution (Sol. PE CUBIC-L: 10 wt % N-butyldiethanolamine, 10 wt % Triton X-100) at 37° C. for approximately 2 days to 4 days.

(4) The mouse organ is washed with PBS several times for several hours per washing.

(5) The mouse organ is immersed, at room temperature overnight, in a clearing CUBIC-R solution (Sol. CL CUBIC-R: 46 wt % antipyrine, 30 wt % nicotinamide) which has been diluted by two folds with use of distilled water.

(6) The mouse organ is immersed in undiluted Sol. CL CUBIC-R for 2 days.

Results of clearing actually performed are shown on the left hand side of FIG. 26 .

(6. Clearing of Mouse Whole Body)

Clearing of the whole body of a mouse can be performed, for example, in accordance with the following procedure.

(1) A mouse whole body is subjected to perfusion fixation with use of 4% paraformaldehyde solution, and then perfused with 100 mL to 200 mL of Sol. PE CUBIC-L.

(2) The mouse whole body is immersed in Sol. PE CUBIC-L at 37° C. for 7 days, during which the liquid is replaced once every 2 days.

(3) The mouse whole body is washed with PBS several times for several hours per washing, and immersed in PBS at room temperature overnight.

(4) The mouse whole body is immersed, at room temperature overnight, in Sol. CL CUBIC-R which has been diluted by 2 folds with use of distilled water.

(5) The mouse whole body is immersed in undiluted Sol. CL CUBIC-R for 2 days.

Results of clearing actually performed are shown at the center of FIG. 26 .

(7. Clearing of Mouse Backbone)

Clearing of the backbone of a mouse can be performed, for example, in accordance with the following procedure.

(1) A backbone of a mouse which has been subjected to perfusion fixation with use of 4% paraformaldehyde solution is taken out, and subjected to post-fixation with use of 4% paraformaldehyde solution at 4° C. overnight.

(2) The mouse backbone is washed with PBS several times for several hours per washing.

(3) The mouse backbone is immersed in Sol. PE CUBIC-L at 37° C. for 3 days.

(4) The mouse backbone is washed with PBS several times for several hours per washing.

(5) The mouse backbone is immersed in a decalcification CUBIC-B solution (Sol. DC CUBIC-B: 10 wt % EDTA, 15 wt % imidazole) at 37° C. for 6 days.

(6) The mouse backbone is washed with PBS several times for several hours per washing.

(7) The mouse backbone is immersed in Sol. PE CUBIC-L at 37° C. for 3 days.

(8) The mouse backbone is washed with PBS several times for several hours per washing.

(9) The mouse backbone is immersed, at room temperature overnight, in Sol. CL CUBIC-R which has been diluted by two folds with use of distilled water.

(10) The mouse backbone is immersed in undiluted Sol. CL CUBIC-R for 2 days.

Results of clearing actually performed are shown on the right hand side of FIG. 26 .

(8. Clearing of Human Tissue)

(1) Human tissue is fixed with use of formalin, immersed in PBS, washed several times for several hours per washing, and immersed in PBS at room temperature overnight.

(2) The human tissue is immersed in Sol. PE at 37° C. for approximately 5 days to 10 days.

(3) The human tissue is washed with PBS several times for several hours per washing, and immersed in PBS at room temperature overnight.

(4) The human tissue is immersed, at room temperature overnight, in Sol. CL CUBIC-R which has been diluted by 2 folds with use of distilled water.

(5) The human tissue is immersed in undiluted Sol. CL CUBIC-R for 2 days.

Results of clearing actually performed are shown in FIG. 27 .

(8. Clearing of Human Brain Tissue)

(1) Human tissue is fixed with use of formalin, immersed in PBS, washed several times for several hours per washing, and immersed in PBS at room temperature overnight.

(2) The human tissue is immersed in Sol. PE CUBIC-HBL solution (Sol. PE CUBIC-HBL: 10 wt % N-butyldiethanolamine, 10 wt % Triton X-100, 15 wt % imidazole) at 37° C. for approximately 5 days to 10 days.

(3) The human tissue is washed with PBS several times for several hours per washing, and immersed in PBS at room temperature overnight.

(4) The human tissue is immersed, at room temperature overnight, in Sol. CL CUBIC-R which has been diluted by 2 folds with use of distilled water.

(5) The human tissue is immersed in undiluted Sol. CL CUBIC-R for 2 days.

A result of clearing actually performed is shown in FIG. 28 .

(10. Clearing of Marmoset Brain)

(1) A brain of a marmoset which has been subjected to perfusion fixation with use of 4% paraformaldehyde solution is taken out, and subjected to post-fixation with use of 4% paraformaldehyde solution at 4° C. overnight.

(2) The marmoset brain is washed with PBS several times for several hours per washing.

(3) The marmoset brain is immersed in Sol. PE CUBIC-L at 37° C. for approximately 21 days, during which the liquid is replaced once every 2 days.

(4) The marmoset brain is immersed in PBS (hereinafter referred to as “AzidoPBS”) containing 0.01% sodium azide at room temperature for 1 week, during which the liquid is replaced every day.

(5) The marmoset brain is immersed in PBS containing 10 μg/mL propidium iodide and 1.5 M NaCl at 37° C. for 12 days.

(6) The marmoset brain is washed by being immersed in AzidoPBS for 2 days, during which the liquid is replaced once every half a day.

(7) The marmoset brain is immersed, at room temperature overnight, in Sol. CL CUBIC-R which has been diluted by 2 folds with use of distilled water.

(8) The marmoset brain is immersed in undiluted Sol. CL CUBIC-R for 4 days.

(9) The marmoset brain is washed by being immersed in AzidoPBS for 2 days, during which the liquid is replaced once every half a day.

(10) The marmoset brain is immersed in 10 wt % imidazole aqueous solution at room temperature for 2 days, during which the liquid is replaced once every half a day.

(11) The marmoset brain is immersed, at room temperature for 4 days, in Sol. CL CUBIC-R (hereinafter referred to as “Sol. CL CUBIC-R2”) which contains 1 wt % #0414 and has been diluted by two folds with use of distilled water.

(12) The marmoset brain is immersed in Sol. CL CUBIC-R2 at room temperature for 7 days, during which the liquid is replaced once.

(13) The marmoset brain is washed by being immersed in AzidoPBS for 2 days, during which the liquid is replaced once every half a day.

(14) The marmoset brain is immersed in Sol. PE CUBIC-L at room temperature for 3 days, then at 37° C. for 2 weeks, and further at 45° C. for 1 week. During this sequence of steps, the liquid is replaced once every 2 days.

(15) The marmoset brain is washed by being immersed in AzidoPBS for 2 days, during which the liquid is replaced once every half a day.

(16) The marmoset brain is immersed in PBS containing 10 μg/mL propidium iodide and 1.5M NaCl at 37° C. for 7 days.

(17) The marmoset brain is washed by being immersed in AzidoPBS for 2 days, during which the liquid is replaced once every half a day.

(18) The marmoset brain is immersed in 10 wt % imidazole aqueous solution at room temperature for 2 days, during which the liquid is replaced once every half a day.

(19) The marmoset brain is immersed, at room temperature for 3 days, in Sol. CL CUBIC-R2 which has been diluted by 2 folds with use of distilled water.

(20) The marmoset brain is immersed in Sol. CL CUBIC-R2 at room temperature for 7 days, during which the liquid is replaced once.

Results of clearing actually performed are shown at the center of FIG. 29 .

TABLE 1 A list of top 50 chemicals with highest delipidation CUBIC ID Chemical name Group CAS no. Chemical structure Detergents #1455 Tween ® 40 Polyether  9005-66-7

#1460 Tween ® 80 Polyether  9005-65-6

#1035 Sodium dodecyl sulfate Anionic detergent  151-21-3

#1419 Sodium 1- undecanesulfonate Anionic detergent  5838-34-6

#0672 Dodecene-1 LAS Anionic detergent 25155-30-0

#1310 Lithium dodecyl sulfate Anionic detergent  2044-56-6

#0865 Sodium nonanoate Anionic detergent 14047-60-0

#0631 (=#0672) Sodium dodecylbenzenesulfonate Anionic detergent 25155-30-0 #0562 Sodium deoxycholate Anionic detergent  302-95-4

#1103 Polyethylene glycol mono-4-octylphenyl ether Polyether  9002-93-1

#1511 Nonidet P-40 Polyether  9016-45-9

#1021 Dodecyltrimethyl- ammonium chloride Cationic detergent  112-00-5

#0703 N-Decanoylsarcosine sodium salt Anionic detergent 30377-07-2

#1466 Sodium N- lauroylsarcosinate Anionic detergent  137-16-6

Triton ™ X-100 Polyether  9002-93-1

#0651 Decyldimethyl(3- sulfopropyl)ammonium Amphiphilic detergent 15163-36-7

#0870 Sodium 1- nonanesulfonate Anionic detergent 35192-74-6

#0566 Sodium Cholate Anionic detergent  361-09-1

#0661 Dodecyldimethyl(3- sulfopropyl)ammonium Amphiphilic detergent 14933-08-5

#1507 (=#0562) Sodium deoxycholate Anionic detergent  302-95-4 #0635 1-Dodecylpyridinium chloride Cationic detergent  104-74-5

#1162 Ammonium pentadecafluorooctanoate Anionic detergent  3825-26-1

#0625 Sodium 1- decanesulfonate Anionic detergent 13419-61-9

#0627 Dodecylamine acetate Cationic detergent 2016-56-0

#1235 Hexadecyltrimethyl- ammonium chloride Cationic detergent  112-02-7

Hydrophilic molecules #1444 1,1,3,3- Tetramethylguanidine Amine   80-70-6

#1456 N,N,N′,N′-Tetramethyl- 1,6-diaminohexane Amine  111-18-2

#1097 Piperidine Amine  110-89-4

#1602 Isophoronediamine Amine  2855-13-2

#1093 Propylamine Amine  107-10-8

#1027 N-Isopropyl-1,3- diaminopropane Amine  3360-16-5

#1267 2-Methyl-1,5- diaminopentane Amine 15520-10-2

#1038 Isoamylamine Amine  107-85-7

#1043 Isobutylamine Amine   78-81-9

#0387 Benzyltrimethyl- ammonium Hydroxide Amine  100-85-6

#0414 N-Butyldiethanolamine Aminoalcohol  102-79-4

#0070 1,3- Bis(aminomethyl) cyclohexane Amine  2579-20-6

#1462 Tropine Aminoalcohol  120-29-6

#1051 1,2-Hexanediol Polyalcohol  6920-22-5

#1541 Allylamine Amine  107-11-9

#0422 N-Butylethylenediamine Amine 19522-69-1

#0441 Benzethonium Chloride Detergent-like aromatic ether  121-54-0

#1008 2,6-Lutidine Pyridine  108-48-5

#0664 6-Dimethylamino-1- hexanol Aminoalcohol  1862-07-3

#0390 N-tert- Butyldiethanolamine Aminoalcohol  2160-93-2

#0071 1,4- Bis(aminomethyl) cyclohexane Amine  2549-93-1

#1006 Isopropylamine Amine   75-31-0

#1312 2,4-Lutidine Pyridine  108-47-4

#1295 1-Methylpyrrolidine Amine  120-94-5

#1074 1-Phenylethane-1,2-diol Polyalcohol   93-56-1

Quadrol ® (Sca/eCUBIC-1)  102-60-3

Triethanolamine (TEA, Sca/eCUBIC-2)  102-71-6

Urea (Sca/e)   57-13-6

PBS 1st quenching assay 1st Relative delipidation assay Fluores- 2nd 2nd quenching assay Cost/unit CUBIC Relative cence of delipidation EGFP (1 g or ID OD600 S.D. Serius S.D. assay fluorescence S.D. OD400 pH Catalog no. 1 mL/yen) Note Detergents #1455 0.073 0.010 0.64 0.05 0.083 6.4 T0544 5.8 #1460 0.095 0.145 0.91 0.01 0.065 5.7 T0546 5.4 #1035 0.106 0.030 1.15 0.05 0.048 6.3 I0352 23.4 #1419 0.124 0.041 1.03 0.00 0.056 5.9 U0031 464 #0672 0.152 0.015 1.08 0.05 0.081 5.9 D1428 7500 #1310 0.155 0.020 1.13 0.01 0.047 6.7 L0254 632 #0865 0.155 0.030 1.03 0.02 0.051 8.9 N0291 220 #0631 (=#0672) 0.163 0.020 0.69 0.01 0.09 6.0 D0990 11 #0562 0.170 0.010 1.08 0.01 0.054 8.3 C0316 268 #1103 0.184 0.080 1.28 0.13 0.051 5.6 P0873 14.2 #1511 0.193 0.015 1.05 0.01 0.057 5.8 Nacalai, @@@ 39 #1021 0.194 0.025 1.11 0.00 0.048 7.5 I0453 105.4 #0703 0.223 0.055 1.03 0.03 0.047 7.0 D2489 2180 #1466 0.237 0.015 1.02 0.00 0.05 6.1 S0597 204 0.240 0.120 1.04 0.02 0.051 5.8 Nacalai, @@@ 14.2 #0651 0.244 0.075 0.97 0.00 0.048 7.5 D4246 1260 #0870 0.247 0.110 1.05 0.03 0.047 6.8 N0311 464 #0566 0.254 0.040 1.07 0.06 0.052 6.7 C0325 84.4 #0661 0.258 0.015 1.13 0.02 0.051 6.5 D3860 352 #1507 (=#0562) 0.303 0.005 1.03 0.00 0.054 7.9 C0316 268 #0635 0.304 0.020 1.04 0.02 0.053 8.9 D0995 45 #1162 0.318 0.020 1.43 0.02 0.048 5.2 P1449 356 #0625 0.325 0.020 0.93 0.25 0.046 5.9 D1181 424 #0627 0.329 0.035 1.05 0.01 0.053 10.3 D0981 384 #1235 0.332 0.090 1.06 0.01 0.048 6.6 H0082 58.8 Hydrophilic #1444 0.124 0.010 0.14 0.01 0.072 12.4 T0148 49.6 #1456 0.135 0.005 0.63 0.02 0.058 12.7 T0537 18.4 #1097 0.166 0.015 0.33 0.00 0.051 13.2 P0453 11.6 #1602 0.190 0.010 0.53 0.01 0.051 10.8 I0228 12.2 #1093 0.208 0.005 0.60 0.03 0.052 13.1 P0520 9.4 #1027 0.219 0.000 0.55 0.02 0.061 13.4 I0420 392 #1267 0.244 0.025 0.51 0.01 0.08 12.9 M0205 8.2 #1038 0.247 0.080 0.30 0.03 0.055 9.6 I0082 78.4 #1043 0.251 0.005 0.48 0.03 0.049 12.0 I0095 11.2 #0387 0.258 0.005 0.00 0.00 0.054 13.8 B1071 39.4 #0414 0.261 0.000 0.70 0.04 0.05 12.7 B0725 15 #0070 0.286 0.015 0.52 0.01 0.079 13.0 B1005 18.8 #1462 0.292 0.000 0.56 0.02 0.053 12.9 T0534 524 #1051 0.300 0.015 0.84 0.05 0.048 9.3 H0688 67 hygro- scopic #1541 0.303 0.015 0.56 0.01 0.068 10.7 A0219 14.2 #0422 0.307 0.085 0.68 0.00 0.05 12.7 B1491 300 hygro- scopic #0441 0.307 0.105 1.08 0.03 0.049 6.4 B0044 41.2 #1008 0.314 0.095 0.71 0.02 0.063 9.9 L0067 19 #0664 0.314 0.085 0.69 0.04 0.062 13.1 D1664 396 #0390 0.318 0.030 0.72 0.01 0.052 12.7 B1194 18.4 #0071 0.318 0.040 0.56 0.00 0.054 13.3 B1083 432 #1006 0.318 0.050 0.58 0.00 0.047 13.1 I0165 6.2 #1312 0.325 0.020 0.84 0.01 0.051 7.6 L0085 32.8 #1295 0.325 0.010 0.66 0.02 0.085 10.5 M0415 32.4 #1074 0.336 0.005 0.58 0.00 0.05 9.5 P0686 203.6 0.569 0.105 0.57 0.01 0.048 12.4 T0781 8.6 0.664 0.030 0.65 0.05 0.048 12.0 S0377 (Wako, 145-05605) 880 (Wako, 3) 0.781 0.025 0.81 0.06 0.048 7.5 U0077 4.7 1.000 0.015 1.00 0.00 0.046 7.9

TABLE 2 A list for 65 chemicals with highest decolorization 700 nm integrated calibrated value Fluorescence quench 420 nm 500-700 nm CUBIC 400 Aver- Aver- Aver- Catalog Cost/ ID Chemical name Group CAS no. Chemical structure nm age S.D. pH age S.D. age S.D. no. unit #0938 1- Ethylimidazole Alkyl- imidazole   7098-07-9

0.053 0.80 0.01 12.1 6.19 0.36 3.41 0.48 E0132 176 1-Methyl- imidazole Alkyl- imidazole   616-47-7 M0508 #0484 1-(3- Aminopropyl) imidazole Alkyl- imidazole   5036-48-6

0.05 0.72 0.03 12.9 4.81 0.02 2.64 0.03 A1185 60.6 #0197 Tris(2- carboxyethyl) phosphine hydrochloride Phosphine  51805-45-9

0.047 −0.05 0.06 2.3 4.28 0.05 3.89 0.06 T1656 3480 #0470 (=#1240) Cetylpyridinium chloride monohydrate Detergent   6004-24-6

0.064 1.06 0.01 8.0 4.20 0.04 3.80 0.03 A5161 (=H0078) 600 #1240 (=#0470) Hexadecyl- pyridinium chloride monohydrate Detergent   6004-24-6 0.05 1.10 0.03 6.9 4.18 0.14 3.84 0.17 H0078 (A5161) 35.2 #0635 1-Dodecyl- pyridinium chloride Detergent   104-74-5

0.053 1.04 0.02 8.9 3.86 0.11 3.57 0.11 D0995 45 #0651 Decyldimethyl (3-sulfopropyl) ammonium hydroxide Detergent  15163-36-7

0.048 0.97 0.00 7.5 3.73 0.15 3.28 0.18 D4246 1260 #0441 Benzethonium chloride Detergent   121-54-0

0.049 1.08 0.03 6.4 3.40 0.24 2.80 0.14 B0044 41.2 #0394 Bis(3- aminopropyl) ether Amine   2157-24-6

0.067 0.54 0.07 13.2 3.27 0.10 1.85 0.00 B1268 3540 #0071 1,4-Bis (aminomethyl) cyclohexane Amine   2549-93-1

0.054 0.56 0.00 13.3 3.25 0.30 1.90 0.21 B1083 432 #0070 1,3-Bis (aminomethyl) cyclohexane Amine   2579-20-6

0.079 0.62 0.01 13.0 3.15 0.04 1.91 0.03 B1005 18.8 #0387 (=#0398) Benzyltrimethyl- ammonium hydroxide Amine   100-85-6

0.054 0.00 0.00 13.8 3.14 0.02 2.56 0.03 B1071 (=B0448) 39.4 #0594 1,8- Diazabicyclo [5.4.0]-7- undecene Amine   6674-22-2

0.05 0.54 0.00 13.5 3.13 0.15 1.94 0.12 D1270 31.4 #1283 N-Methyl- nicotinamide Pyridine   114-33-0

0.063 0.71 0.03 10.7 2.98 0.16 2.81 0.11 M0374 356 #1235 Hexadecyl- trimethyl- ammonium Chloride Detergent   112-02-7

0.048 1.06 0.01 6.6 2.85 0.28 2.71 0.47 H0082 58.8 #0389 N-Benzyl- ethanolamine Amino- alcohol   104-63-2

0.063 0.57 0.01 10.9 2.73 0.02 2.42 0.05 B1130 21.6 #0007 6-Amino-1- hexanol Amino- alcohol   4048-33-3

0.093 0.22 0.20 11.9 2.66 0.05 1.76 0.05 A1027 756 #0370 2-Amino-6- methylpyridine Pyridine   1824-81-3

0.064 0.67 0.01 11.3 2.66 0.28 2.57 0.26 A0403 30.6 #0664 6- Dimethylamino- 1-hexanol Amino- alcohol   1862-07-3

0.062 0.69 0.04 13.1 2.64 0.07 2.72 0.08 D1664 396 #0855 Nicotinamide Pyridine    98-92-0

0.052 0.75 0.01 10.4 2.63 0.05 2.45 0.07 N0078 12.8 #0380 3,3′-Diamino-N- methyldipropyl- amine Amine   105-83-9

0.065 0.62 0.03 13.0 2.62 0.05 1.58 0.03 B0821 16.6 #1312 2,4-Lutidine Pyridine   108-47-4

0.051 0.84 0.01 7.6 2.47 0.02 2.59 0.01 L0085 32.8 #1102 3-Picolylamine Pyridine   3731-52-0

0.056 0.77 0.02 11.6 2.46 0.05 1.32 0.04 P0762 42.4 #1575 2-Diethylamino- ethanol Amino- alcohol   100-37-8

0.06 0.61 0.00 12.8 2.41 0.22 1.21 0.10 D0465 5.8 #0587 1,5-Diazabicyclo [4.3.0]-5-nonene Amine   3001-72-7

0.049 0.72 0.01 12.6 2.41 0.04 1.38 0.03 D1313 156.8 #0694 (=#0661) Dodecyldimethyl (3-sulfopropyl) ammonium hydroxide Detergent  14933-08-5

0.055 1.09 0.03 8.4 2.24 0.09 2.53 0.72 D2332 (=D3860) 137.2 #0783 1,4- Diaminobutane Amine   110-60-1

0.05 0.60 0.00 14.0 2.21 0.00 1.42 0.02 D0239 22.75 #0627 Dodecylamine acetate Detergent   2016-56-0

0.053 1.05 0.01 10.3 2.21 0.03 1.74 0.02 D0981 384 #1226 1-(2- Hydroxyethyl)- 4-(3- hydroxypropyl) piperidine Amino- alcohol  19780-85-9

0.05 0.76 0.01 14.1 2.20 0.08 2.29 0.14 H0360 368 #1456 N,N,N′,N′- Tetramethyl-1,6- diaminohexane Amine   111-18-2

0.058 0.63 0.02 12.7 2.17 0.48 2.11 0.47 T0537 18.4 #0362 Benzyldimethyl- tetradecyl- ammonium chloride hydrate Detergent   139-08-2

0.053 1.07 0.00 6.6 2.13 0.12 1.74 0.06 A0208 32.6 #0661 (=#0694) Dodecyldimethyl (3-sulfopropyl) ammonium hydroxide Detergent  14933-08-5 0.051 1.13 0.02 6.5 2.10 0.10 1.70 0.11 D3860 (=D2332) 352 #0785 3,3′-Diamino- dipropylamine Amine    56-18-8

0.05 0.62 0.01 13.8 2.09 0.05 1.48 0.04 D0090 17.4 #0398 (=#0387) Benzyltrimethyl- ammonium hydroxide   100-85-6 0.054 0.00 0.00 12.9 2.09 0.03 1.77 0.05 B0448 (=B1071) 16.4 #1602 Isophoronediamine Amine   2855-13-2

0.051 0.53 0.01 10.8 2.08 0.32 1.26 0.18 I0228 12.2 #0652 1,1′-Dimethyl- 4,4′- bipyridinium dichloride Pyridine   1910-42-5

0.082 0.42 0.01 6.0 2.01 0.12 2.01 0.14 D3685 2480 #1008 2,6-Lutidine Pyridine   108-48-5

0.063 0.71 0.02 9.9 2.00 0.10 2.16 0.07 L0067 19 #1021 Dodecyltrimethyl- ammonium chloride Detergent   112-00-5

0.048 1.11 0.00 7.5 1.96 0.08 1.70 0.11 I0453 105.4 #0003 5-Amino-1- pentanol Amino- alcohol   2508-29-4

0.052 0.63 0.01 12.5 1.83 0.22 1.21 0.17 A0875 182.8 #0678 1,3- Diaminopentane Amine   589-37-7

0.049 0.60 0.01 13.6 1.71 0.04 1.15 0.04 D2252 23.8 #1027 N-Isopropyl-1,3- diaminopropane Amine   3360-16-5

0.061 0.55 0.02 13.4 1.52 0.07 1.24 0.11 I0420 392 #0467 4-Aminomethyl- tetrahydropyran Amine 130290-79-8

0.049 0.65 0.01 12.9 1.52 0.14 1.13 0.19 A2550 4400 #1267 2-Methyl-1,5- diaminopentane Amine  15520-10-2

0.08 0.51 0.01 12.9 1.48 0.09 1.09 0.09 M0205 8.2 #1367 5-Bromo-1- pentanol Alcohol  34626-51-2

0.055 −0.01 0.00 2.9 1.48 0.00 0.06 0.06 B1848 920 #1422 Veratryl alcohol Alcohol    93-03-8

0.05 0.89 0.04 6.1 1.46 0.52 1.28 0.56 V0020 308 #0672 Dodecene- 1 LAS (JIS K 3363- 1990) Detergent  25155-30-0

0.081 1.08 0.05 5.9 1.45 0.04 1.41 0.04 D1428 7500 #1086 Pyrazine Pyridine   290-37-9

0.051 0.67 0.01 8.6 1.41 0.13 1.39 0.15 P0544 64.8 #0779 N,N-Diethyl- ethylenediamine Amine   100-36-7

0.051 0.70 0.02 13.6 1.39 0.04 0.81 0.01 D0505 21.6 #1167 1-(2-Pyrimidyl) piperazine Amine  20980-22-7

0.084 0.01 0.01 12.5 1.39 0.06 1.09 0.07 P1110 412 #1455 Tween ® 40 Detergent   9005-66-7

0.083 0.64 0.05 6.4 1.38 0.45 1.21 0.40 T0544 5.6 #1444 1,1,3,3-Tetra- methylguanidine Amine    80-70-6

0.072 0.14 0.01 12.4 1.38 0.12 1.15 0.08 T0148 49.6 #0414 N-Butyl- diethanolamine Amino- alcohol   102-79-4

0.05 0.70 0.04 12.7 1.30 0.00 1.45 0.06 B0725 15 #1537 N,N,N′,N′- Tetrakis(2- hydroxyethyl) ethylenediamine Amino- alcohol   140-07-8

0.048 0.66 0.01 11.7 1.29 0.11 1.63 0.18 T0120 184 #1035 Sodium dodecyl sulfate Detergent   151-21-3

0.048 1.15 0.05 6.3 1.28 0.34 1.32 0.42 I0352 23.4 #1507 (=#0562) Sodium deoxycholate Detergent   302-95-4

0.054 1.03 0.00 7.9 1.27 0.01 1.03 0.04 C0316 268 #0788 N,N-Dimethyl- benzamide Benzyl amide   611-74-5

0.049 0.76 0.00 10.7 1.26 0.16 1.08 0.16 D0256 66.8 #0640 2,3-Dimethyl-1- phenyl-5- pyrazolone Pyra- zolone    60-80-0

0.048 0.84 0.01 7.5 1.22 0.27 0.93 0.25 D1876 27.2 #0006 4-Amino-1- butanol Amino- alcohol  13325-10-5

0.06 0.64 0.03 12.3 1.22 0.00 0.82 0.02 A1013 1172 #1105 N,N,N′,N″,N″- Pentakis(2- hydroxypropyl) diethylene- triamine Amino- alcohol  17121-34-5

0.057 0.74 0.04 13.2 1.20 0.10 1.05 0.11 P0832 49.6 #0277 N,N′-Bis(3- aminopropyl) ethylenediamine Amine  10563-26-5

0.053 0.71 0.01 13.1 1.20 0.02 0.83 0.01 B1952 16.6 #0562 (=#1507) Sodium deoxycholate Detergent   302-95-4 0.054 1.08 0.01 8.3 1.18 0.04 0.98 0.03 C0316 268 #1061 1-(2- Hydroxyethyl) ethyleneimine Amino- alcohol   1072-52-2

0.048 0.80 0.02 13.1 1.14 0.04 0.91 0.02 H0567 444 #0425 Benzyltriphenyl- phosphonium chloride Phosphine   1100-88-5

0.048 0.35 0.01 9.3 1.14 0.02 0.83 0.01 B0824 43.2 #1062 1,3-Diamino- 2-propanol Amino- alcohol   616-29-5

0.054 0.67 0.03 12.8 1.13 0.26 0.80 0.11 H0497 656

TABLE 3 A list of top 27 chemicals with highest RI and water-solubility 1st quenching 1st RI assay evaluation Relative 2nd quenching assay Cost/ assay Fluores- Chem- unit RI of cence ical EGFP (1 g or CUBIC 10% of conc. fluores- Catalog 1 mL/ ID Chemical name Group CAS no. Chemical structure chemical Serius S.D. (wt %) RI cence S.D. OD400 pH no. yen) #0640 2,3-Dimethyl- 1-phenyl-5- pyrazolone Benzyl amine   60-80-0

1.3549 0.84 0.01 60 1.4966 quench free 0.048 7.5 D1876 27.2 #1612 Xylazine hydrochloride Benzyl amine  23076-35-9

1.3519 0.97 0.00 70 1.4956 0.053 5.8 X0059 1480 #0370 2-Amino-6- methylpyridine Pyridine  1824-81-3

1.3555 0.67 0.01 70 1.4922 0.064 11.3 A0403 30.6 #1140 2-Methyl- pyridine N-oxide Pyridine   931-19-1

1.3511 1.04 0.00 70 1.4919 0.049 6.2 P0418 74 #0830 S-[2- (Dimethyl- amino)ethyl] isothiourea- dihydrochloride Amine  16111-27-6

1.3527 1.06 0.02 70 1.5021 0.047 5.4 D0652 510 #1181 Phthalimide DBU salt Amine 119812-51-0

1.3526 0.94 0.00 @ @ 0.049 6.0 P1235 404 #0809 Diphen- hydramine hydrochloride Benzyl amine   147-24-0

1.3526 0.90 0.00 70 1.4990 0.048 7.0 D0423 59.4 #0450 Benzyl- dimethyl- phenyl- ammonium chloride Benzyl amine  3204-68-0

1.3525 0.72 0.02 70 1.5002 quench free 0.052 6.7 B0416 308 #1142 DL- Phenylephrine hydrochloride Benzyl amino- alcohol   154-86-9

1.3539 0.93 0.04 70 1.4954 0.066 5.7 P0397 432 #1145 4- Methylpyridine N-oxide Pyridine  1003-67-4

1.3538 0.98 0.03 70 1.5073 0.059 7.3 P0420 252 #1283 N-Methyl- nicotinamide Pyridine   114-33-0

1.3522 0.71 0.03 70 1.4902 quench free 0.063 10.7 M0374 356 #1392 Tolperisone hydrochloride Benzyl amine  3644-61-9

1.3522 0.69 0.01 70 1.4939 0.056 5.2 T1319 164 #0299 Bis(2-dimethyl- aminoethyl) disulfide dihydrochloride Amine  17339-60-5

1.3523 1.04 0.01 70 1.4937 0.047 5.3 B2272 184 #1102 3-Picolylamine Pyridine  3731-52-0

1.3527 0.77 0.02 70 1.4895 0.056 11.6 P0762 42.4 #0864 Neostigmine bromide Benzyl amine   114-80-7

1.3503 0.99 0.02 70 1.4830 quench free 0.051 6.0 N0358 704 #1052 Hydrazine carbonate Hydrazine 112077-84-6 H₂N—NH₂ H₂CO₃ 1.3510 1.04 0.03 70 1.4799 quench free 0.047 10.2 H0854 15.4 #0788 N,N- Dimethyl- benzamide Benzyl amide   611-74-5

1.3505 0.76 0.00 70 1.4833 quench free 0.049 10.7 D0256 66.8 #0389 N-Benzyl- ethanolamine Benzyl amino- alcohol   104-63-2

1.3524 0.57 0.01 70 1.4814 quench free 0.063 10.9 B1130 21.6 #0307 Benzyltributyl- ammonium chloride Benzyl amine  23616-79-7

1.3507 0.90 0.03 80 1.4939 0.048 7.0 B1384 27.8 #0587 1,5- Diazabicyclo [4.3.0]-5- nonene Amine  3001-72-7

1.3501 0.72 0.01 75 1.4836 0.049 12.6 D1313 156.8 #0338 N-(2- Aminoethyl) piperazine Amine   140-31-8

1.3507 0.66 0.02 75 1.4794 0.062 12.4 A0304 9.8 #0315 1-Butyl- pyridinium bromide Pyridine   874-80-6

1.3504 1.11 0.01 85 1.5090 0.048 5.6 B1743 488 #0609 N,N-Diethyl- nicotinamide Pyridine   59-26-7

1.3502 1.03 0.01 80 1.4928 0.056 6.4 D0514 62.8 #1078 Pyridine N- oxide Pyridine   694-59-7

1.3518 0.98 0.00 60 1.4795 0.054 6.1 P0557 55.8 #0785 3,3′-Diamino- dipropylamine Amine   56-18-8

1.3502 0.62 0.01 100 1.4895 0.050 13.8 D0090 17.4 #0415 1-Butyl- pyridinium chloride Pyridine  1124-64-7

1.3505 0.99 0.00 90 1.4824 0.055 5.5 B1329 556 #0637 1,3-Dimethyl- thiourea Urea   534-13-4

1.3555 1.05 0.01 @ @ 0.049 6.8 D0804 30.6 Diatrizoic acid (FocusClear ™)   737-31-5

#DIV/0! #DIV/0! D1462 296 #0956 D-Glucamine (FocusClear ™)   488-43-7

1.3475 0.42 0.01 0.260 12.3 G0252 603 D-(−)-Fructose (SeeDB)   57-48-7

#DIV/0! #DIV/0! F0060 6.6 D-(+)-Sucrose (CUBIC-2)   57-50-1

1.3472 0.92 0.01 0.048 6.5 S0111 4.8 Histodenz ™ (RIMS)  66108-95-0

1.3490 0.84 0.03 0.054 7.3 D2158 (SIGMA) 501 PBS 1.3350 1.00 0.00 0.046 7.9

TABLE 4 Group 1: Halogenated monocarboxylic acid #0062 5-Chlorovaleric acid  

  pH 2.86, score 0.92 #0074 5-Bromovaleric acid  

  pH 2.39, score 0.94 #1162 Ammonium pentadecafluoro- octanoate  

  pH 5.24, score 0.95 #1577 Dichloroacetic acid  

  pH 2.29, score 0 Group 2: Hydroxymonocarboxylic acid #0155 3-Hydroxypropionic acid  

  pH 3.66, score 0.91 #0175 3-Hydroxycyclohexane carboxylic acid  

  pH 4.22, score 0.92 #1307 DL-Lactic acid  

  pH 2.14, score 0.78 Group 3: Aliphatic monocarboxylic acid #0073 3-Butenoic acid  

  pH 3.43, score 0.82 #1569 Cyanoacetic acid  

  pH 2.61, score 0.52 Group 4: Alkyl amino monocarboxylic acid #0454 Betaine hydrochloride  

  pH 2.07, score 0.31 #0702 3-(Dimethylamino) propionic acid hydrochloride  

  pH 2.17, score 0.91 Group 5: Acetylamino monocarboxylic acid #0346 N-Acetyl- L-cysteine  

  pH 2.86, score 0.94 #0360 N-Acetyl- DL-methionine  

  pH 2.75, score 0.94 #0350 N-Acetyl- L-methionine  

  pH 2.74, score 0.94 #0741 N-Chloroacetyl glycine  

  pH 2.43, score 0.87 #0965 DL-Pyro glutamic acid  

  pH 2.33, score 0.86 #1071 L-Pyro glutamic acid  

  pH 3.01, score 0.86 Group 6: Other monocarboxylic acids #0473 1-Aminocyclobutanecarboxylic acid hydrochloride  

  pH 2.18, score 0.84 #0534 4-Chloro-DL-mandelic acid  

  pH 2.49, score 0.62 #0712 Cetirizine dihydrochloride  

  pH 3.59, score 0.95 #0746 2-Chloro-L-mandelic acid  

  pH 2.14, score 0.91 #0916 4-[(4-Methyl-1-piperazinyl) methyl]benzoic acid dihydrochloride  

  pH 2.80, score 0.93 #0942 N-Formylglycine  

  pH 2.67, score 0.77 #1108 Ozagrel hydrochloride hydrate  

  pH 4.92, score 0.88 #1249 4-Guanidino benzoic acid hydrochloride  

  pH 4.22, score 0.91 #1328 3-Bromopyruvic acid  

  pH 2.13, score 0.67 Group 7: Dicarboxylic acid #1305 Malonic acid  

  pH 2.33, score 0.32 Group 8: Malic acid #1300 DL-Malic acid  

  pH 2.34, score 0.42 Group 9: Thiodicarboxylic acid #1302 Thiomalic acid  

  pH 2.68, score 0.85 Group 10: Tartaric acid #0621 2-(Dimethylamino)ethanol L-(+)-bitartrate  

  pH 4.43, score 0.93 #0749 L-Carnitine L-tartrate  

  pH 4.65, score 0.93 #1428 DL-Tartaric acid  

  pH 2.18, score 0.49 #1594 Nicotine bi-L-(+)- tartrate dihydrate  

  pH 4.84, score 0.71 Group 11: Malonic acid #0762 Cyclopentyl malonic acid  

  pH 2.74, score 0.53 Group 12: Other dicarboxylic acids #0936 Ethylenediamine-N,N′- dipropionic acid dihydrochloride  

  pH 2.22, score 0.88 Group 13: Polyvalent carboxylic acid #0692 Diammonium ethylene- diaminetetraacetate monohydrate  

  pH 4.97, score 0.92 #1094 1,2,3-Propanetri- carboxylic acid  

  pH 2.69, score 0.91 Group 14: Sugars #0963 D-(+)-Glucono-1,5-lactone  

  pH 2.69, score 0.88 #1010 Lactobionic acid  

  pH 2.63, score 0.95 #1203 D-Glucuronic acid  

  pH 2.04, score 0.70 #1534 Gluconic Acid  

  pH 2.60, score 0.91 Group 15: Tetrafluoroborate #1156 Pottasium phenyl trifloroborate  

  pH 3.60, score 0.35 #1562 2-Bromo-1-ethylpyridinium tetrafluoroborate  

  pH 3.92, score 0.50 #1598 [(Oxido)phenyl(trifluoromethyl)-λ⁴- sulfanylidene]dimethylammonium tetrafluoroborate  

  pH 4.52, score 0.93 #1608 N-Fluoro-N′-(chloromethyl) triethylenediamine bis (tetrafluoroborate)  

  pH 5.19, score 0.26 #1609 Tetraethylammonium tetrafluoroborate  

  pH 4.03, score 0.45 Group 16: Phosphonic acids #1004 Isopropyl phosphate  

  pH 2.40, score 0 Group 17: Sulfonic acids #0745 L-cysteic acid  

  pH 2.11, score 0.44 #1165 Pyridine-3-sulfonic acid  

  pH 2.21, score 0.89 #1213 DL-Homocysteinethiolactone hydrochloride  

  pH 2.31, score 0.94 Group 18: Hydrocarbon #0216 Ethyl trans-4-hydroxy- cyclohexanecarboxylate  

  pH 5.68, score 0.94 #1109 1,2-Octanediol  

  pH 6.00, score 0.95 #1365 4-Chloro-1-butanol (contains tetrahydrofuran)  

  pH 3.08, score 0.87 #1366 4-Bromo-1-butanol (contains tetrahydrofuran)  

  pH 2.31, score 0.63 Group 19: Amines #0071 1,4-Bis(aminomethyl) cyclohexane  

  pH 13.27, score 0.94 #0480 1-(2-Aminoethyl)-4-methyl- piperazine hydrochloride  

  pH 2.67, score 0.63 #1390 1,4,7-Triazacyclononane trihydrochloride  

  pH 2.08, score 0.89 Group 20: Hydrazine #1280 Methylhydrazine sulfate CH₃NHNH₂•H₂SO₄ pH 2.09, score 0.74 Group 21: Aromatic amine #0429 O-Benzylhydroxylamine hydrochloride  

  pH 4.10, score 0.24 #1610 o-Toluidine hydrochloride  

  pH 4.23, score 0.94 Base chemical #1439 N,N,N′,N′-Tetramethylethylenediamine  

INDUSTRIAL APPLICABILITY

The present invention is applicable, for example, to a high-throughput observation of gene expression, cellular localization, and cell morphology within a whole tissue. 

1-3. (canceled)
 4. A method for preparing a biological material having an excellent light-transmitting property, the method comprising the step of: causing a solution to permeate into a biological material, the solution containing a compound which is soluble at a concentration of 60 wt % or more in water and which allows an aqueous solution, in which the compound (D) is contained at a concentration that is at least one value within a range of 60 wt % to 80 wt %, to have a refractive index of 1.47 to 1.50.
 5. The method as set forth in claim 4, wherein the compound is at least one selected from the group consisting of a benzylamine, a pyridine, an amine, a benzylaminoalcohol, hydrazine, and thiourea.
 6. The method as set forth in claim 4, wherein the compound is at least one selected from the group consisting of benzylamine, 2,3-dimethyl-1-phenyl-5-pyrazolone, xylazine hydrochloride, 2-amino-6-methylpyridine, 2-methylpyridine N-oxide, S-[2-(dimethylamino)ethyl]isothiourea dihydrochloride, phthalimide DBU salt, diphenhydramine hydrochloride, benzyldimethylphenylammoniumchloride, DL-phenylephrine hydrochloride, 4-methylpyridine N-oxide, N-methylnicotinamide, tolperisone hydrochloride, bis(2-dimethylaminoethyl)disulfide dihydrochloride, 3-picolylamine, neostigmine bromide, hydrazine carbonate, N,N-dimethylbenzamide, N-benzylethanolamine, benzyltributylammonium chloride, 1,5-diazabicyclo[4.3.0]-5-nonene, N-(2-aminoethyl)piperazine, 1-butylpyridine bromide, N,N-diethylnicotinamide, pyridine N-oxide, 3,3′-diaminodipropylamine, 1-butylpyridinium chloride, 1,3-dimethylthiourea, diatrizonic acid, D-glucamine, D-(−)-fructose, D-(+)-sucrose, Histodenz™, and PBS.
 7. The method as set forth in claim 4, wherein the compound is at least one selected from the group consisting of 2,3-dimethyl-1-phenyl-5-pyrazolone, xylazine hydrochloride, 2-amino-6-methylpyridine, 2-methylpyridine N-oxide, 5-[2-(dimethylamino)ethyl]isothiourea dihydrochloride, phthalimide DBU salt, diphenhydramine hydrochloride, benzyldimethylphenylammoniumchloride, DL-phenylephrine hydrochloride, 4-methylpyridine N-oxide, N-methylnicotinamide, tolperisone hydrochloride, bis(2-dimethylaminoethyl)disulfide dihydrochloride, 3-picolylamine, neostigmine bromide, hydrazine carbonate, N,N-dimethylbenzamide, N-benzylethanolamine, benzyltributylammonium chloride, 1,5-diazabicyclo[4.3.0]-5-nonene, N-(2-aminoethyl)piperazine, 1-butylpyridine bromide, N,N-diethylnicotinamide, pyridine N-oxide, 3,3′-diaminodipropylamine, 1-butylpyridinium chloride, 1,3-dimethylthiourea, diatrizonic acid, D-glucamine, D-(−)-fructose, D-(+)-sucrose, Histodenz™, and PBS.
 8. The method as set forth in claim 4, wherein the compound is at least one selected from the group consisting of 2-amino-6-methylpyridine, N-benzylethanolamine, 1,5-diazabicyclo[4.3.0]-5-nonene, N,N-diethylnicotinamide, 2,3-dimethyl-1-phenyl-5-pyrazolone, 3-picolylamine, and N-methylnicotinamide.
 9. The method as set forth in claim 4, wherein the compound is at least one selected from the group consisting of benzylamine, 2,3-dimethyl-1-phenyl-5-pyrazolone, N-methylnicotinamide, 1,5-diazabicyclo[4.3.0]-5-nonene, and 3-picolylamine. 